Forecasting in the presence of level shifts

This article addresses the problem of forecasting time series that are subject to level shifts. Processes with level shifts possess a nonlinear dependence structure. Using the stochastic permanent breaks (STOPBREAK) model, I model this nonlinearity in a direct and flexible way that avoids imposing a discrete regime structure. I apply this model to the rate of price inflation in the United States, which I show is subject to level shifts. These shifts significantly affect the accuracy of out‐of‐sample forecasts, causing models that assume covariance stationarity to be substantially biased. Models that do not assume covariance stationarity, such as the random walk, are unbiased but lack precision in periods without shifts. I show that the STOPBREAK model outperforms several alternative models in an out‐of‐sample inflation forecasting experiment. Copyright © 2005 John Wiley & Sons, Ltd.     

Modelling the long QT syndrome with induced pluripotent stem cells

The ability to generate patient-specific human induced pluripotent stem cells (iPSCs) offers a new paradigm for modelling human disease and for individualizing drug testing. Congenital long QT syndrome (LQTS) is a familial arrhythmogenic syndrome characterized by abnormal ion channel function and sudden cardiac death. Here we report the development of a patient/disease-specific human iPSC line from a patient with type-2 LQTS (which is due to the A614V missense mutation in the KCNH2 gene). The generated iPSCs were coaxed to differentiate into the cardiac lineage. Detailed whole-cell patch-clamp and extracellular multielectrode recordings revealed significant prolongation of the action-potential duration in LQTS human iPSC-derived cardiomyocytes (the characteristic LQTS phenotype) when compared to healthy control cells. Voltage-clamp studies confirmed that this action-potential-duration prolongation stems from a significant reduction of the cardiac potassium current I(Kr). Importantly, LQTS-derived cells also showed marked arrhythmogenicity, characterized by early-after depolarizations and triggered arrhythmias. We then used the LQTS human iPSC-derived cardiac-tissue model to evaluate the potency of existing and novel pharmacological agents that may either aggravate (potassium-channel blockers) or ameliorate (calcium-channel blockers, K(ATP)-channel openers and late sodium-channel blockers) the disease phenotype. Our study illustrates the ability of human iPSC technology to model the abnormal functional phenotype of an inherited cardiac disorder and to identify potential new therapeutic agents. As such, it represents a promising paradigm to study disease mechanisms, optimize patient care (personalized medicine), and aid in the development of new therapies.     

A single positively selected West Nile viral mutation confers increased virogenesis in American crows

West Nile virus (WNV), first recognized in North America in 1999, has been responsible for the largest arboviral epiornitic and epidemic of human encephalitis in recorded history. Despite the well-described epidemiological patterns of WNV in North America, the basis for the emergence of WNV-associated avian pathology, particularly in the American crow (AMCR) sentinel species, and the large scale of the North American epidemic and epiornitic is uncertain. We report here that the introduction of a T249P amino acid substitution in the NS3 helicase (found in North American WNV) in a low-virulence strain was sufficient to generate a phenotype highly virulent to AMCRs. Furthermore, comparative sequence analyses of full-length WNV genomes demonstrated that the same site (NS3-249) was subject to adaptive evolution. These phenotypic and evolutionary results provide compelling evidence for the positive selection of a mutation encoding increased viremia potential and virulence in the AMCR sentinel bird species.     

Fresnel's laws,ceteris paribus

This article is about structural realism, historical continuity, laws of nature, and ceteris paribus clauses. Fresnel's Laws of optics support Structural Realism because they are a scientific structure that has survived theory change. However, the history of Fresnel's Laws which has been depicted in debates over realism since the 1980s is badly distorted. Specifically, claims that J. C. Maxwell or his followers believed in an ontologically-subsistent electromagnetic field, and gave up the aether, before Einstein's annus mirabilis in 1905 are indefensible. Related claims that Maxwell himself did not believe in a luminiferous aether are also indefensible. This paper corrects the record. In order to trace Fresnel's Laws across significant ontological changes, they must be followed past Einstein into modern physics and nonlinear optics. I develop the philosophical implications of a more accurate history, and analyze Fresnel's Laws' historical trajectory in terms of dynamic ceteris paribus clauses. Structuralists have not embraced ceteris paribus laws, but they continue to point to Fresnel's Laws to resist anti-realist arguments from theory change. Fresnel's Laws fit the standard definition of a ceteris paribus law as a law applicable only in particular circumstances. Realists who appeal to the historical continuity of Fresnel's Laws to combat anti-realists must incorporate ceteris paribus laws into their metaphysics.     

Mantle compensation of active metamorphic core complexes at Woodlark rift in Papua New Guinea

In many highly extended rifts on the Earth, tectonic removal of the upper crust exhumes mid-crustal rocks, producing metamorphic core complexes. These structures allow the upper continental crust to accommodate tens of kilometres of extension, but it is not clear how the lower crust and underlying mantle respond. Also, despite removal of the upper crust, such core complexes remain both topographically high and in isostatic equilibrium. Because many core complexes in the western United States are underlain by a flat Moho discontinuity, it has been widely assumed that their elevation is supported by flow in the lower crust or by magmatic underplating. These processes should decouple upper-crust extension from that in the mantle. In contrast, here we present seismic observations of metamorphic core complexes of the western Woodlark rift that show the overall crust to be thinned beneath regions of greatest surface extension. These core complexes are actively being exhumed at a rate of 5-10 km Myr(-1), and the thinning of the underlying crust appears to be compensated by mantle rocks of anomalously low density, as indicated by low seismic velocities. We conclude that, at least in this case, the development of metamorphic core complexes and the accommodation of high extension is not purely a crustal phenomenon, but must involve mantle extension.     

Synthetic biology: engineering Escherichia coli to see light

We have designed a bacterial system that is switched between different states by red light. The system consists of a synthetic sensor kinase that allows a lawn of bacteria to function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition (about 100 megapixels per square inch), two-dimensional chemical image. This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps.     

Clonal selection drives genetic divergence of metastatic medulloblastoma

Medulloblastoma, the most common malignant paediatric brain tumour, arises in the cerebellum and disseminates through the cerebrospinal fluid in the leptomeningeal space to coat the brain and spinal cord. Dissemination, a marker of poor prognosis, is found in up to 40% of children at diagnosis and in most children at the time of recurrence. Affected children therefore are treated with radiation to the entire developing brain and spinal cord, followed by high-dose chemotherapy, with the ensuing deleterious effects on the developing nervous system. The mechanisms of dissemination through the cerebrospinal fluid are poorly studied, and medulloblastoma metastases have been assumed to be biologically similar to the primary tumour. Here we show that in both mouse and human medulloblastoma, the metastases from an individual are extremely similar to each other but are divergent from the matched primary tumour. Clonal genetic events in the metastases can be demonstrated in a restricted subclone of the primary tumour, suggesting that only rare cells within the primary tumour have the ability to metastasize. Failure to account for the bicompartmental nature of metastatic medulloblastoma could be a major barrier to the development of effective targeted therapies.     

Terahertz-field-induced insulator-to-metal transition in vanadium dioxide metamaterial

Electron-electron interactions can render an otherwise conducting material insulating, with the insulator-metal phase transition in correlated-electron materials being the canonical macroscopic manifestation of the competition between charge-carrier itinerancy and localization. The transition can arise from underlying microscopic interactions among the charge, lattice, orbital and spin degrees of freedom, the complexity of which leads to multiple phase-transition pathways. For example, in many transition metal oxides, the insulator-metal transition has been achieved with external stimuli, including temperature, light, electric field, mechanical strain or magnetic field. Vanadium dioxide is particularly intriguing because both the lattice and on-site Coulomb repulsion contribute to the insulator-to-metal transition at 340?K (ref. 8). Thus, although the precise microscopic origin of the phase transition remains elusive, vanadium dioxide serves as a testbed for correlated-electron phase-transition dynamics. Here we report the observation of an insulator-metal transition in vanadium dioxide induced by a terahertz electric field. This is achieved using metamaterial-enhanced picosecond, high-field terahertz pulses to reduce the Coulomb-induced potential barrier for carrier transport. A nonlinear metamaterial response is observed through the phase transition, demonstrating that high-field terahertz pulses provide alternative pathways to induce collective electronic and structural rearrangements. The metamaterial resonators play a dual role, providing sub-wavelength field enhancement that locally drives the nonlinear response, and global sensitivity to the local changes, thereby enabling macroscopic observation of the dynamics. This methodology provides a powerful platform to investigate low-energy dynamics in condensed matter and, further, demonstrates that integration of metamaterials with complex matter is a viable pathway to realize functional nonlinear electromagnetic composites.