Closure of population biobanks and direct-to-consumer genetic testing companies

Genetic research gained new momentum with the completion of the Human Genome Project in 2003. Formerly centered on the investigation of single-gene disorders, genetic research is increasingly targeting common complex diseases and in doing so is studying the whole genome, the environment and its impact on genomic variation. Consequently, biobanking initiatives have emerged around the world as a tool to sustain such progress. Whether they are small scale or longitudinal, public or private, commercial or non-commercial, biobanks should consider the possibility of closure. Interestingly, while raising important ethical issues, this topic has hardly been explored in the literature. Indeed, ethical issues associated with sale, insolvency, end of funding, or transfer of materials to other entities (which are all issues either related to or possible consequences of closure) are seldom the subject of discussion. In an attempt to fill this gap, this paper will discuss-using population and direct-to-consumer (DTC) genetic testing companies' biobanks as case studies-(1) international and national normative documents addressing the issue of closure and (2) the internal policies of population biobanks and DTC genetic testing companies. The analysis will inform the debate on biobank closure and elucidate the underlying ethical issues, which include, but are not limited to informed consent, storage and privacy

Using an Ellipsoid Model to Track and Predict the Evolution and Propagation of Coronal Mass Ejections

We present a method for tracking and predicting the propagation and evolution of coronal mass ejections (CMEs) using the imagers on the STEREO and SOHO satellites. By empirically modeling the material between the inner core and leading edge of a CME as an expanding, outward propagating ellipsoid, we track its evolution in three-dimensional space. Though more complex empirical CME models have been developed, we examine the accuracy of this relatively simple geometric model, which incorporates relatively few physical assumptions, including i) a constant propagation angle and ii) an azimuthally symmetric structure. Testing our ellipsoid model developed herein on three separate CMEs, we find that it is an effective tool for predicting the arrival of density enhancements and the duration of each event near 1 AU. For each CME studied, the trends in the trajectory, as well as the radial and transverse expansion are studied from 0 to ~.3 AU to create predictions at 1 AU with an average accuracy of 2.9 hours.Comment: 18 pages, 11 figure

Branching and annihilating Levy flights

We consider a system of particles undergoing the branching and annihilating reactions A -> (m+1)A and A + A -> 0, with m even. The particles move via long-range Levy flights, where the probability of moving a distance r decays as r^{-d-sigma}. We analyze this system of branching and annihilating Levy flights (BALF) using field theoretic renormalization group techniques close to the upper critical dimension d_c=sigma, with sigma<2. These results are then compared with Monte-Carlo simulations in d=1. For sigma close to unity in d=1, the critical point for the transition from an absorbing to an active phase occurs at zero branching. However, for sigma bigger than about 3/2 in d=1, the critical branching rate moves smoothly away from zero with increasing sigma, and the transition lies in a different universality class, inaccessible to controlled perturbative expansions. We measure the exponents in both universality classes and examine their behavior as a function of sigma.Comment: 9 pages, 4 figure

Phase transition classes in triplet and quadruplet reaction diffusion models

Phase transitions of reaction-diffusion systems with site occupation restriction and with particle creation that requires n=3,4 parents, whereas explicit diffusion of single particles (A) is present are investigated in low dimensions by mean-field approximation and simulations. The mean-field approximation of general nA -> (n+k)A, mA -> (m-l)A type of lattice models is solved and novel kind of critical behavior is pointed out. In d=2 dimensions the 3A -> 4A, 3A -> 2A model exhibits a continuous mean-field type of phase transition, that implies d_c<2 upper critical dimension. For this model in d=1 extensive simulations support a mean-field type of phase transition with logarithmic corrections unlike the Park et al.'s recent study (Phys. Rev E {\bf 66}, 025101 (2002)). On the other hand the 4A -> 5A, 4A -> 3A quadruplet model exhibits a mean-field type of phase transition with logarithmic corrections in d=2, while quadruplet models in 1d show robust, non-trivial transitions suggesting d_c=2. Furthermore I show that a parity conserving model 3A -> 5A, 2A->0 in d=1 has a continuous phase transition with novel kind of exponents. These results are in contradiction with the recently suggested implications of a phenomenological, multiplicative noise Langevin equation approach and with the simulations on suppressed bosonic systems by Kockelkoren and Chat\'e (cond-mat/0208497).Comment: 8 pages, 10 figures included, Updated with new data, figures, table, to be published in PR

Modeling the Longitudinal Asymmetry in Sunspot Emergence -- the Role of the Wilson Depression

The distributions of sunspot longitude at first appearance and at disappearance display an east-west asymmetry that results from a reduction in visibility as one moves from disk centre to the limb. To first order, this is explicable in terms of simple geometrical foreshortening. However, the centre-to-limb visibility variation is much larger than that predicted by foreshortening. Sunspot visibility is also known to be affected by the Wilson effect: the apparent dish shape of the sunspot photosphere caused by the temperature-dependent variation of the geometrical position of the tau=1 layer. In this article we investigate the role of the Wilson effect on the sunspot appearance distributions, deducing a mean depth for the umbral tau=1 layer of 500 to 1500 km. This is based on the comparison of observations of sunspot longitude distribution and Monte Carlo simulations of sunspot appearance using different models for spot growth rate, growth time and depth of Wilson depression.Comment: 18 pages, 10 figures, in press (Solar Physics

The large longitudinal spread of solar energetic particles during the January 17, 2010 solar event

We investigate multi-spacecraft observations of the January 17, 2010 solar energetic particle event. Energetic electrons and protons have been observed over a remarkable large longitudinal range at the two STEREO spacecraft and SOHO suggesting a longitudinal spread of nearly 360 degrees at 1AU. The flaring active region, which was on the backside of the Sun as seen from Earth, was separated by more than 100 degrees in longitude from the magnetic footpoints of each of the three spacecraft. The event is characterized by strongly delayed energetic particle onsets with respect to the flare and only small or no anisotropies in the intensity measurements at all three locations. The presence of a coronal shock is evidenced by the observation of a type II radio burst from the Earth and STEREO B. In order to describe the observations in terms of particle transport in the interplanetary medium, including perpendicular diffusion, a 1D model describing the propagation along a magnetic field line (model 1) (Dr\"oge, 2003) and the 3D propagation model (model 2) by (Dr\"oge et al., 2010) including perpendicular diffusion in the interplanetary medium have been applied, respectively. While both models are capable of reproducing the observations, model 1 requires injection functions at the Sun of several hours. Model 2, which includes lateral transport in the solar wind, reveals high values for the ratio of perpendicular to parallel diffusion. Because we do not find evidence for unusual long injection functions at the Sun we favor a scenario with strong perpendicular transport in the interplanetary medium as explanation for the observations.Comment: The final publication is available at http://www.springerlink.co

Novel universality class of absorbing transitions with continuously varying critical exponents

The well-established universality classes of absorbing critical phenomena are directed percolation (DP) and directed Ising (DI) classes. Recently, the pair contact process with diffusion (PCPD) has been investigated extensively and claimed to exhibit a new type of critical phenomena distinct from both DP and DI classes. Noticing that the PCPD possesses a long-term memory effect, we introduce a generalized version of the PCPD (GPCPD) with a parameter controlling the memory effect. The GPCPD connects the DP fixed point to the PCPD point continuously. Monte Carlo simulations show that the GPCPD displays novel type critical phenomena which are characterized by continuously varying critical exponents. The same critical behaviors are also observed in models where two species of particles are coupled cyclically. We suggest that the long-term memory may serve as a marginal perturbation to the ordinary DP fixed point.Comment: 13 pages + 10 figures (Full paper version

Instability, Intermixing and Electronic Structure at the Epitaxial LaAlO3/SrTiO3(001) Heterojunction

The question of stability against diffusional mixing at the prototypical LaAlO3/SrTiO3(001) interface is explored using a multi-faceted experimental and theoretical approach. We combine analytical methods with a range of sensitivities to elemental concentrations and spatial separations to investigate interfaces grown using on-axis pulsed laser deposition. We also employ computational modeling based on the density function theory as well as classical force fields to explore the energetic stability of a wide variety of intermixed atomic configurations relative to the idealized, atomically abrupt model. Statistical analysis of the calculated energies for the various configurations is used to elucidate the relative thermodynamic stability of intermixed and abrupt configurations. We find that on both experimental and theoretical fronts, the tendency toward intermixing is very strong. We have also measured and calculated key electronic properties such as the presence of electric fields and the value of the valence band discontinuity at the interface. We find no measurable electric field in either the LaAlO3 or SrTiO3, and that the valence band offset is near zero, partitioning the band discontinuity almost entirely to the conduction band edge. Moreover, we find that it is not possible to account for these electronic properties theoretically without including extensive intermixing in our physical model of the interface. The atomic configurations which give the greatest electrostatic stability are those that eliminate the interface dipole by intermixing, calling into question the conventional explanation for conductivity at this interface - electronic reconstruction. Rather, evidence is presented for La indiffusion and doping of the SrTiO3 below the interface as being the cause of the observed conductivity

Bringing Proportional Recovery into Proportion: Bayesian Modelling of Post-Stroke Motor Impairment

Accurate predictions of motor impairment after stroke are of cardinal importance for the patient, clinician, and health care system. More than ten years ago, the proportional recovery rule was introduced by promising just that: high-fidelity predictions of recovery following stroke based only on the initially lost motor function, at least for a specific fraction of patients. However, emerging evidence suggests that this recovery rule is subject to various confounds and may apply less universally than previously assumed. Here, we systematically revisited stroke outcome predictions by applying strategies to avoid confounds and fitting hierarchical Bayesian models. We jointly analyzed n=385 post-stroke trajectories from six separate studies – one of the currently largest overall datasets of upper limb motor recovery. We addressed confounding ceiling effects by introducing a subset approach and ensured correct model estimation through synthetic data simulations. Subsequently, we used model comparisons to assess the underlying nature of recovery within our empirical recovery data. The first model comparison, relying on the conventional fraction of patients called fitters, pointed to a combination of proportional to lost function and constant recovery. Proportional to lost here describes the original notion of proportionality, indicating greater recovery in case of a more severe initial impairment. This combination explained only 32% of the variance in recovery, which is in stark contrast to previous reports of >80%. When instead analyzing the complete spectrum of subjects, fitters and non-fitters, a combination of proportional to spared function and constant recovery was favoured, implying a more significant improvement in case of more preserved function. Explained variance was at 53%. Therefore, our quantitative findings suggest that motor recovery post-stroke may exhibit some characteristics of proportionality. However, the variance explained was substantially reduced compared to what has previously been reported. This finding motivates future research moving beyond solely behavior scores to explain stroke recovery and establish robust and discriminating single-subject predictions