Theoretical Design and Analysis of Multivolume Digital Assays with Wide Dynamic Range Validated Experimentally with Microfluidic Digital PCR

This paper presents a protocol using theoretical methods and free software to design and analyze multivolume digital PCR (MV digital PCR) devices; the theory and software are also applicable to design and analysis of dilution series in digital PCR. MV digital PCR minimizes the total number of wells required for “digital” (single molecule) measurements while maintaining high dynamic range and high resolution. In some examples, multivolume designs with fewer than 200 total wells are predicted to provide dynamic range with 5-fold resolution similar to that of single-volume designs requiring 12 000 wells. Mathematical techniques were utilized and expanded to maximize the information obtained from each experiment and to quantify performance of devices and were experimentally validated using the SlipChip platform. MV digital PCR was demonstrated to perform reliably, and results from wells of different volumes agreed with one another. No artifacts due to different surface-to-volume ratios were observed, and single molecule amplification in volumes ranging from 1 to 125 nL was self-consistent. The device presented here was designed to meet the testing requirements for measuring clinically relevant levels of HIV viral load at the point-of-care (in plasma, 1 000 000 molecules/mL), and the predicted resolution and dynamic range was experimentally validated using a control sequence of DNA. This approach simplifies digital PCR experiments, saves space, and thus enables multiplexing using separate areas for each sample on one chip, and facilitates the development of new high-performance diagnostic tools for resource-limited applications. The theory and software presented here are general and are applicable to designing and analyzing other digital analytical platforms including digital immunoassays and digital bacterial analysis. It is not limited to SlipChip and could also be useful for the design of systems on platforms including valve-based and droplet-based platforms. In a separate publication by Shen et al. (J. Am. Chem. Soc., 2011, DOI: 10.1021/ja2060116), this approach is used to design and test digital RT-PCR devices for quantifying RNA

Implicitly Priming the Social Brain: Failure to Find Neural Effects

Humans have a fundamental need for social relationships. Rejection from social groups is especially detrimental, rendering the ability to detect threats to social relationships and respond in adaptive ways critical. Indeed, previous research has shown that experiencing social rejection alters the processing of subsequent social cues in a variety of socially affiliative and avoidant ways. Because social perception and cognition occurs spontaneously and automatically, detecting threats to social relationships may occur without conscious awareness or control. Here, we investigated the automaticity of social threat detection by examining how implicit primes affect neural responses to social stimuli. However, despite using a well- established implicit priming paradigm and large sample size, we failed to find any evidence that implicit primes induced changes at the neural level. That implicit primes influence behavior has been demonstrated repeatedly and across a variety of domains, and our goal is not to question these effects. Rather, we offer the present study as cautionary evidence that such a paradigm may not be amenable to scanning in an fMRI environment

Characterisation of damage mechanisms in oxide ceramics indented at dynamic and quasi-static strain rates

Ceramic materials are known to display rate dependent behaviour under impact. Tests to establish the strain-rate dependent variations in damage mechanisms have been carried out on debased alumina, an alumina-zirconia composite, and 3Y-TZP. Materials were indented dynamically and quasi-statically using identical sharp hardened steel projectiles while recording the load profile. Characteristics typical of both sharp and blunt indentation types were observed using scanning electron microscopy and piezospectroscopic mapping. At dynamic strain rates both the depth of the indentation and the residual stress in the material were lower than for quasi-static tests. This was attributed to temperature-induced softening of the projectile. Unusual behaviour was observed in the 3Y-TZP samples due to the reversible transformation from tetragonal to monoclinic crystal structures during mechanical loading. These effects and the observed superior mechanical strength against impact suggest that zirconia or zirconia-composite materials may have advantages over debased alumina for application as ceramic armour materials

Comparing periodic-orbit theory to perturbation theory in the asymmetric infinite square well

An infinite square well with a discontinuous step is one of the simplest systems to exhibit non-Newtonian ray-splitting periodic orbits in the semiclassical limit. This system is analyzed using both time-independent perturbation theory (PT) and periodic-orbit theory and the approximate formulas for the energy eigenvalues derived from these two approaches are compared. The periodic orbits of the system can be divided into classes according to how many times they reflect from the potential step. Different classes of orbits contribute to different orders of PT. The dominant term in the second-order PT correction is due to non-Newtonian orbits that reflect from the step exactly once. In the limit in which PT converges the periodic-orbit theory results agree with those of PT, but outside of this limit the periodic-orbit theory gives much more accurate results for energies above the potential step.Comment: 22 pages, 2 figures, 2 tables, submitted to Physical Review

Environments for sonic ecologies

This paper outlines a current lack of consideration for the environmental context of Evolutionary Algorithms used for the generation of music. We attempt to readdress this balance by outlining the benefits of developing strong coupling strategies between agent and en- vironment. It goes on to discuss the relationship between artistic process and the viewer and suggests a placement of the viewer and agent in a shared environmental context to facilitate understanding of the artistic process and a feeling of participation in the work. The paper then goes on to outline the installation ‘Excuse Me and how it attempts to achieve a level of Sonic Ecology through the use of a shared environmental context

UV Imaging Polarimetry of the peculiar Seyfert 2 galaxy Mrk 477

We present the results of UV imaging polarimetry of the Seyfert 2 galaxy Mrk 477 taken by the Faint Object Camera onboard the Hubble Space Telescope (HST). From a previous HST UV image (lambda ~ 2180A), Mrk 477 has been known to have a pointlike bright UV hotspot in the central region, peculiar among nearby Seyfert 2 galaxies. There are also claims of UV/optical variability, unusual for a Seyfert 2 galaxy. Our data show that there is an off-nuclear scattering region ~ 0."6 (~ 500 pc) NE from the hotspot. The data, after the subtraction of the instrumental effect due to this bright hotspot region, might indicate that the scattered light is also detected in the central 0."2 radius region and is extended to a very wide angle. The hotspot location is consistent with the symmetry center of the PA pattern, which represents the location of the hidden nucleus, but our data do not provide a strong upper limit to the distance between the symmetry center and the hotspot. We have obtained high spatial resolution color map of the continuum which shows that the nuclear spiral arm of 0."4 scale (~ 300pc) is significantly bluer than the off-nuclear mirror and the hotspot region. The nature of the hotspot is briefly discussed.Comment: To appear in Ap

Insights into a dinoflagellate genome through expressed sequence tag analysis

BACKGROUND: Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging. RESULTS: Approximately 20% of the 6,723 unique (11,171 total 3'-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair. CONCLUSION: This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production

Systematic review of the clinical effectiveness and cost-effectiveness, and economic evaluation, of denosumab for the treatment of bone metastases from solid tumours

Peer reviewedPublisher PD

High Energy Cosmic-ray Diffusion in Molecular Clouds: A Numerical Approach

The propagation of high-energy cosmic rays through giant molecular clouds constitutes a fundamental process in astronomy and astrophysics. The diffusion of cosmic-rays through these magnetically turbulent environments is often studied through the use of energy-dependent diffusion coefficients, although these are not always well motivated theoretically. Now, however, it is feasible to perform detailed numerical simulations of the diffusion process computationally. While the general problem depends upon both the field structure and particle energy, the analysis may be greatly simplified by dimensionless analysis. That is, for a specified purely turbulent field, the analysis depends almost exclusively on a single parameter -- the ratio of the maximum wavelength of the turbulent field cells to the particle gyration radius. For turbulent magnetic fluctuations superimposed over an underlying uniform magnetic field, particle diffusion depends on a second dimensionless parameter that characterizes the ratio of the turbulent to uniform magnetic field energy densities. We consider both of these possibilities and parametrize our results to provide simple quantitative expressions that suitably characterize the diffusion process within molecular cloud environments. Doing so, we find that the simple scaling laws often invoked by the high-energy astrophysics community to model cosmic-ray diffusion through such regions appear to be fairly robust for the case of a uniform magnetic field with a strong turbulent component, but are only valid up to $\sim 50$ TeV particle energies for a purely turbulent field. These results have important consequences for the analysis of cosmic-ray processes based on TeV emission spectra associated with dense molecular clouds.Comment: Accepted for publication in The Astrophysical Journa