Variational data assimilation using targetted random walks

The variational approach to data assimilation is a widely used methodology for both online prediction and for reanalysis (offline hindcasting). In either of these scenarios it can be important to assess uncertainties in the assimilated state. Ideally it would be desirable to have complete information concerning the Bayesian posterior distribution for unknown state, given data. The purpose of this paper is to show that complete computational probing of this posterior distribution is now within reach in the offline situation. In this paper we will introduce an MCMC method which enables us to directly sample from the Bayesian\ud posterior distribution on the unknown functions of interest, given observations. Since we are aware that these\ud methods are currently too computationally expensive to consider using in an online filtering scenario, we frame this in the context of offline reanalysis. Using a simple random walk-type MCMC method, we are able to characterize the posterior distribution using only evaluations of the forward model of the problem, and of the model and data mismatch. No adjoint model is required for the method we use; however more sophisticated MCMC methods are available\ud which do exploit derivative information. For simplicity of exposition we consider the problem of assimilating data, either Eulerian or Lagrangian, into a low Reynolds number (Stokes flow) scenario in a two dimensional periodic geometry. We will show that in many cases it is possible to recover the initial condition and model error (which we describe as unknown forcing to the model) from data, and that with increasing amounts of informative data, the uncertainty in our estimations reduces

Reducing the stress of drug administration:implications for the 3Rs

Restraint in animals is known to cause stress but is used during almost all scientific procedures in rodents, representing a major welfare and scientific issue. Administration of substances, a key part of most scientific procedures, almost always involves physical restraint of the animal. In this study, we developed a method to inject substances to rats using a non-restrained technique. We then compared the physiological, behavioral and emotional impacts of restrained versus non-restrained injection procedures. Our results highlight the negative welfare implications associated with physical restraint and demonstrate a method which can be used to avoid this. Our work shows how adopting strategies that avoid restraint can minimize a widespread source of stress in laboratory animals and improve welfare through refinement

Lower semicontinuity of attractors for non-autonomous dynamical systems

This paper is concerned with the lower semicontinuity of attractors for semilinear non-autonomous differential equations in Banach spaces. We require the unperturbed attractor to be given as the union of unstable manifolds of time-dependent hyperbolic solutions, generalizing previous results valid only for gradient-like systems in which the hyperbolic solutions are equilibria. The tools employed are a study of the continuity of the local unstable manifolds of the hyperbolic solutions and results on the continuity of the exponential dichotomy of the linearization around each of these solutions

Blending the Old and the New: Qualitative Data Analysis a s Critical Thinking and Using NVivo with a Generic Approach

In this article the authors seek to make the case that qualitative data analysis can be explained within the framework of critical thinking and incorporates within this framework the role of technology – specifically NVivo. First they discuss critical thinking from the perspectives of Bloom, Adler, and Polanyi. They then link critical thinking to the concept of a general inductive approach to qualitative analysis as described by Thomas. Finally, they illustrate connections of both critical thinking and the general inductive approach to technology using NVivo screenshots

Downward shortwave surface irradiance from 17 sites for the FIRE/SRB Wisconsin experiment

A field experiment was conducted in Wisconsin during Oct. to Nov. 1986 for purposes of both intensive cirrus cloud measurments and SRB algorithm validation activities. The cirrus cloud measurements were part of the FIRE. Tables are presented which show data from 17 sites in the First ISCCP (International Satellite Cloud Climatology Project) Regional Experiment/Surface Radiation Budget (FIRE/SRB) Wisconsin experiment region. A discussion of intercomparison results and calibration inconsistencies is also included

Production and characterization of anti-human interferon γ receptor antibody fragments that inhibit cytokine binding to the receptor

Three single-chain antibody fragments that recognize the extracellular human interferon γ receptor α-chain (IFNγR), and inhibit the binding of human IFNγ, have been produced in Escherichia coli. These fragments are derived from murine anti-receptor monoclonal antibodies, and comprise the variable heavy (VH) domain linked to the variable light (VL) chain through a 15 amino acid linker [(GGGGS)3]. Using surface plasmon resonance technology (BIAcore), the soluble proteins were shown to retain a high affinity for recombinant IFNγR, and by radioimmunoassay to possess high inhibitory activity towards IFNγ-binding to human Raji cells. The antibody fragments most likely recognize epitopes that overlap the cytokine binding site on the receptor surface. Attempts to dissect further the antibodies to isolated VH- and VL-chains and to synthetic linear and cyclic peptides derived from the individual complementarity determining regions failed to afford fragments with significant IFNγR binding affinity. Nevertheless, these native-like variable region fragments and petidomimetics derived from them are of interest in the design of novel IFNγR antagonist

Snake prices and crocodile appetites: Aquatic wildlife supply and demand on Tonle Sap Lake, Cambodia

Commercial trade is a major driver of over-exploitation of wild species, but the pattern of demand and how it responds to changes in supply is poorly understood. Here we explore the markets for snakes from Tonle Sap Lake in Cambodia to evaluate future exploitation scenarios, identify entry points for conservation and, more generally, to illustrate the value of multi-scale analysis of markets to traded wildlife conservation. In Cambodia, the largest driver of snake exploitation is the domestic trade in snakes as crocodile food. We estimate that farmed crocodiles consume between 2.7 and 12.2 million snakes per year. The market price for crocodiles has been in decline since 2003, which, combined with rising prices for their food, has led to a reduced frequency of feeding and closure of small farms. The large farms that generate a disproportionate amount of the demand for snakes continue to operate in anticipation of future market opportunities, and preferences for snakes could help maintain demand if market prices for crocodiles rise to pre 2003 levels. In the absence of a sustained demand from crocodile farms, it is also possible that alternative markets will develop, such as one for human snack food. The demand for snakes, however, also depends on the availability of substitute resources, principally fish. The substitutability and low price elasticity of demand offers a relatively sustainable form of consumerism. Given the nature of these market drivers, addressing consumer preferences and limiting the protection of snakes to their breeding season are likely to be the most effective tools for conservation. This study highlights the importance of understanding the structure of markets and the behaviour of consumer demand prior to implementing regulations on wildlife hunting and trade

Rapid-acting antidepressant drugs modulate affective bias in rats

How rapid-acting antidepressants (RAADs), such as ketamine, induce immediate and sustained improvements in mood in patients with major depressive disorder (MDD) is poorly understood. A core feature of MDD is the prevalence of cognitive processing biases associated with negative affective states, and the alleviation of negative affective biases may be an index of response to drug treatment. Here, we used an affective bias behavioral test in rats, based on an associative learning task, to investigate the effects of RAADs. To generate an affective bias, animals learned to associate two different digging substrates with a food reward in the presence or absence of an affective state manipulation. A choice between the two reward-associated digging substrates was used to quantify the affective bias generated. Acute treatment with the RAADs ketamine, scopolamine, or psilocybin selectively attenuated a negative affective bias in the affective bias test. Low, but not high, doses of ketamine and psilocybin reversed the valence of the negative affective bias 24 hours after RAAD treatment. Only treatment with psilocybin, but not ketamine or scopolamine, led to a positive affective bias that was dependent on new learning and memory formation. The relearning effects of ketamine were dependent on protein synthesis localized to the rat medial prefrontal cortex and could be modulated by cue reactivation, consistent with experience-dependent neural plasticity. These findings suggest a neuropsychological mechanism that may explain both the acute and sustained effects of RAADs, potentially linking their effects on neural plasticity with affective bias modulation in a rodent model

Matching post-Newtonian and numerical relativity waveforms: systematic errors and a new phenomenological model for non-precessing black hole binaries

We present a new phenomenological gravitational waveform model for the inspiral and coalescence of non-precessing spinning black hole binaries. Our approach is based on a frequency domain matching of post-Newtonian inspiral waveforms with numerical relativity based binary black hole coalescence waveforms. We quantify the various possible sources of systematic errors that arise in matching post-Newtonian and numerical relativity waveforms, and we use a matching criteria based on minimizing these errors; we find that the dominant source of errors are those in the post-Newtonian waveforms near the merger. An analytical formula for the dominant mode of the gravitational radiation of non-precessing black hole binaries is presented that captures the phenomenology of the hybrid waveforms. Its implementation in the current searches for gravitational waves should allow cross-checks of other inspiral-merger-ringdown waveform families and improve the reach of gravitational wave searches.Comment: 22 pages, 11 figure