Direct detection and characterization of foot-and-mouth disease virus in East Africa using a field-ready real-time PCR platform

Effective control and monitoring of foot-and-mouth disease (FMD) relies upon rapid and accurate disease confirmation. Currently, clinical samples are usually tested in reference laboratories using standardized assays recommended by The World Organisation for Animal Health (OIE). However, the requirements for prompt and serotype-specific diagnosis during FMD outbreaks, and the need to establish robust laboratory testing capacity in FMD-endemic countries have motivated the development of simple diagnostic platforms to support local decision-making. Using a portable thermocycler, the T-COR™ 8, this study describes the laboratory and field evaluation of a commercially available, lyophilized pan-serotype-specific real-time RT-PCR (rRT-PCR) assay and a newly available FMD virus (FMDV) typing assay (East Africa-specific for serotypes: O, A, Southern African Territories [SAT] 1 and 2). Analytical sensitivity, diagnostic sensitivity and specificity of the pan-serotype-specific lyophilized assay were comparable to that of an OIE-recommended laboratory-based rRT-PCR (determined using a panel of 57 FMDV-positive samples and six non-FMDV vesicular disease samples for differential diagnosis). The FMDV-typing assay was able to correctly identify the serotype of 33/36 FMDV-positive samples (no cross-reactivity between serotypes was evident). Furthermore, the assays were able to accurately detect and type FMDV RNA in multiple sample types, including epithelial tissue suspensions, serum, oesophageal–pharyngeal (OP) fluid and oral swabs, both with and without the use of nucleic acid extraction. When deployed in laboratory and field settings in Tanzania, Kenya and Ethiopia, both assays reliably detected and serotyped FMDV RNA in samples (n = 144) collected from pre-clinical, clinical and clinically recovered cattle. These data support the use of field-ready rRT-PCR platforms in endemic settings for simple, highly sensitive and rapid detection and/or characterization of FMDV

Explaining Evidence Denial as Motivated Pragmatically Rational Epistemic Irrationality

This paper introduces a model for evidence denial that explains this behavior as a manifestation of rationality and it is based on the contention that social values (measurable as utilities) often underwrite these sorts of responses. Moreover, it is contended that the value associated with group membership in particular can override epistemic reason when the expected utility of a belief or belief system is great. However, it is also true that it appears to be the case that it is still possible for such unreasonable believers to reverse this sort of dogmatism and to change their beliefs in a way that is epistemically rational. The conjecture made here is that we should expect this to happen only when the expected utility of the beliefs in question dips below a threshold where the utility value of continued dogmatism and the associated group membership is no longer sufficient to motivate defusing the counter-evidence that tells against such epistemically irrational beliefs

A probabilistic analysis of argument cogency

This paper offers a probabilistic treatment of the conditions for argument cogency as endorsed in informal logic: acceptability, relevance, and sufficiency. Treating a natural language argument as a reason-claim-complex, our analysis identifies content features of defeasible argument on which the RSA conditions depend, namely: change in the commitment to the reason, the reason’s sensitivity and selectivity to the claim, one’s prior commitment to the claim, and the contextually determined thresholds of acceptability for reasons and for claims. Results contrast with, and may indeed serve to correct, the informal understanding and applications of the RSA criteria concerning their conceptual dependence, their function as update-thresholds, and their status as obligatory rather than permissive norms, but also show how these formal and informal normative approachs can in fact align

The three-dimensional Anderson model of localization with binary random potential

We study the three-dimensional two-band Anderson model of localization and compare our results to experimental results for amorphous metallic alloys (AMA). Using the transfer-matrix method, we identify and characterize the metal-insulator transitions as functions of Fermi level position, band broadening due to disorder and concentration of alloy composition. The appropriate phase diagrams of regions of extended and localized electronic states are studied and qualitative agreement with AMA such as Ti-Ni and Ti-Cu metallic glasses is found. We estimate the critical exponents nu_W, nu_E and nu_x when either disorder W, energy E or concentration x is varied, respectively. All our results are compatible with the universal value nu ~ 1.6 obtained in the single-band Anderson model.Comment: 9 RevTeX4 pages with 11 .eps figures included, submitted to PR

Critical Dynamics of a Vortex Loop Model for the Superconducting Transition

We calculate analytically the dynamic critical exponent $z_{MC}$ measured in Monte Carlo simulations for a vortex loop model of the superconducting transition, and account for the simulation results. In the weak screening limit, where magnetic fluctuations are neglected, the dynamic exponent is found to be $z_{MC} = 3/2$. In the perfect screening limit, $z_{MC} = 5/2$. We relate $z_{MC}$ to the actual value of $z$ observable in experiments and find that $z \sim 2$, consistent with some experimental results

Nature of the Low Field Transition in the Mixed State of High Temperature Superconductors

We have numerically studied the statics and dynamics of a model three-dimensional vortex lattice at low magnetic fields. For the statics we use a frustrated 3D XY model on a stacked triangular lattice. We model the dynamics as a coupled network of overdamped resistively-shunted Josephson junctions with Langevin noise. At low fields, there is a weakly first-order phase transition, at which the vortex lattice melts into a line liquid. Phase coherence parallel to the field persists until a sharp crossover, conceivably a phase transition, near $T_{\ell} > T_m$ which develops at the same temperature as an infinite vortex tangle. The calculated flux flow resistivity in various geometries near $T=T_{\ell}$ closely resembles experiment. The local density of field induced vortices increases sharply near $T_\ell$, corresponding to the experimentally observed magnetization jump. We discuss the nature of a possible transition or crossover at $T_\ell$(B) which is distinct from flux lattice melting.Comment: Updated references. 46 pages including low quality 25 eps figures. Contact [email protected] or visit http://www.physics.ohio-state.edu:80/~ryu/ for better figures and additional movie files from simulations. To be published in Physical Review B1 01Jun9

Facts, Values and Quanta

Quantum mechanics is a fundamentally probabilistic theory (at least so far as the empirical predictions are concerned). It follows that, if one wants to properly understand quantum mechanics, it is essential to clearly understand the meaning of probability statements. The interpretation of probability has excited nearly as much philosophical controversy as the interpretation of quantum mechanics. 20th century physicists have mostly adopted a frequentist conception. In this paper it is argued that we ought, instead, to adopt a logical or Bayesian conception. The paper includes a comparison of the orthodox and Bayesian theories of statistical inference. It concludes with a few remarks concerning the implications for the concept of physical reality.Comment: 30 pages, AMS Late

Critical scaling of the a.c. conductivity for a superconductor above Tc

We consider the effects of critical superconducting fluctuations on the scaling of the linear a.c. conductivity, \sigma(\omega), of a bulk superconductor slightly above Tc in zero applied magnetic field. The dynamic renormalization- group method is applied to the relaxational time-dependent Ginzburg-Landau model of superconductivity, with \sigma(\omega) calculated via the Kubo formula to O(\epsilon^{2}) in the \epsilon = 4 - d expansion. The critical dynamics are governed by the relaxational XY-model renormalization-group fixed point. The scaling hypothesis \sigma(\omega) \sim \xi^{2-d+z} S(\omega \xi^{z}) proposed by Fisher, Fisher and Huse is explicitly verified, with the dynamic exponent z \approx 2.015, the value expected for the d=3 relaxational XY-model. The universal scaling function S(y) is computed and shown to deviate only slightly from its Gaussian form, calculated earlier. The present theory is compared with experimental measurements of the a.c. conductivity of YBCO near Tc, and the implications of this theory for such experiments is discussed.Comment: 16 pages, submitted to Phys. Rev.

Magnetic phases and reorientation transitions in antiferromagnetically coupled multilayers

In antiferromagnetically coupled superlattices grown on (001) faces of cubic substrates, e.g. based on materials combinations as Co/Cu, Fe/Si, Co/Cr, or Fe/Cr, the magnetic states evolve under competing influence of bilinear and biquadratic exchange interactions, surface-enhanced four-fold in-plane anisotropy, and specific finite-size effects. Using phenomenological (micromagnetic) theory, a comprehensive survey of the magnetic states and reorientation transitions has been carried out for multilayer systems with even number of ferromagnetic sub-layers and magnetizations in the plane. In two-layer systems (N=2) the phase diagrams in dependence on components of the applied field in the plane include ``swallow-tail'' type regions of (metastable) multistate co-existence and a number of continuous and discontinuous reorientation transitions induced by radial and transversal components of the applied field. In multilayers (N \ge 4) noncollinear states are spatially inhomogeneous with magnetization varying across the multilayer stack. For weak four-fold anisotropy the magnetic states under influence of an applied field evolve by a complex continuous reorientation into the saturated state. At higher anisotropy they transform into various inhomogeneous and asymmetric structures. The discontinuous transitions between the magnetic states in these two-layers and multilayers are characterized by broad ranges of multi-phase coexistence of the (metastable) states and give rise to specific transitional domain structures.Comment: Manuscript 34 pages, 14 figures; submitted for publicatio

Using airborne LiDAR Survey to explore historic-era archaeological landscapes of Montserrat in the eastern Caribbean

This article describes what appears to be the first archaeological application of airborne LiDAR survey to historic-era landscapes in the Caribbean archipelago, on the island of Montserrat. LiDAR is proving invaluable in extending the reach of traditional pedestrian survey into less favorable areas, such as those covered by dense neotropical forest and by ashfall from the past two decades of active eruptions by the Soufrière Hills volcano, and to sites in localities that are inaccessible on account of volcanic dangers. Emphasis is placed on two aspects of the research: first, the importance of ongoing, real-time interaction between the LiDAR analyst and the archaeological team in the field; and second, the advantages of exploiting the full potential of the three-dimensional LiDAR point cloud data for purposes of the visualization of archaeological sites and features