Use of stereo camera systems for assessment of rockfish abundance in untrawlable areas and for recording pollock behavior during midwater trawls

We describe the application of two types of stereo camera systems in fisheries research, including the design, calibration, analysis techniques, and precision of the data obtained with these systems. The first is a stereo video system deployed by using a quick-responding winch with a live feed to provide species- and size- composition data adequate to produce acoustically based biomass estimates of rockfish. This system was tested on the eastern Bering Sea slope where rockfish were measured. Rockfish sizes were similar to those sampled with a bottom trawl and the relative error in multiple measurements of the same rockfish in multiple still-frame images was small. Measurement errors of up to 5.5% were found on a calibration target of known size. The second system consisted of a pair of still-image digital cameras mounted inside a midwater trawl. Processing of the stereo images allowed fish length, fish orientation in relation to the camera platform, and relative distance of the fish to the trawl netting to be determined. The video system was useful for surveying fish in Alaska, but it could also be used broadly in other situations where it is difficult to obtain species-composition or size-composition information. Likewise, the still-image system could be used for fisheries research to obtain data on size, position, and orientation of fish

Benchmark all-electron ab initio quantum Monte Carlo calculations for small molecules

We study the efficiency, precision and accuracy of all-electron variational and diffusion quantum Monte Carlo calculations using Slater basis sets. Starting from wave functions generated by Hartree-Fock and density functional theory, we describe an algorithm to enforce the electron-nucleus cusp condition by linear projection. For the 55 molecules in the G2 set, the diffusion quantum Monte Carlo calculations recovers an average of 95% of the correlation energy and reproduces bond energies to a mean absolute deviation of 3.2 kcal/mol. Comparing the individual total energies with essentially exact values, we investigate the error cancellation in atomization and chemical reaction path energies, giving additional insight into the sizes of nodal surface errors.Comment: 7 pages, 7 figures, published by J. Chem. Phys (substantial changes after first submission

The effectiveness of delineation treatments

A literature review undertaken for Transit NZ has found that delineation has a significant effect on driver behaviour with, for example, shoulder rumble strips reducing run-off-theroad crashes by between 22% and 80% (average of 32% for all crashes and 44% for fatal run-of-the-road crashes). The concern that enhancing roadway delineation may sometimes be accompanied by an unwanted increase in drivers’ speeds (known as behavioural adaptation) is not borne out by the research and appears to be a phenomenon associated with a few restricted situations (e.g. where a centre line is added to an otherwise unmarked road). The preponderance of the evidence supports the conclusion that profiled edge lines and centre lines provide drivers with positive guidance and produce significant reductions in crashes as a result of improving drivers’ lateral position. Further, unlike other safety measures that show decreased effectiveness over time due to a novelty effect, profiled lane delineation continues to work regardless of driver familiarity. There is no published research to suggest that profiled edge lines will decrease the effectiveness of a profiled centre line or will result in an increase in crash rates or an increase in the severity of crashes. However it has also been noted that local conditions have a major influence on the level of benefits that can be achieved through improved delineation

Timescales for dynamical relaxation to the Born rule

We illustrate through explicit numerical calculations how the Born-rule probability densities of non-relativistic quantum mechanics emerge naturally from the particle dynamics of de Broglie-Bohm pilot-wave theory. The time evolution of a particle distribution initially not equal to the absolute square of the wave function is calculated for a particle in a two-dimensional infinite potential square well. Under the de Broglie-Bohm ontology, the box contains an objectively-existing 'pilot wave' which guides the electron trajectory, and this is represented mathematically by a Schroedinger wave function composed of a finite out-of-phase superposition of M energy eigenstates (with M ranging from 4 to 64). The electron density distributions are found to evolve naturally into the Born-rule ones and stay there; in analogy with the classical case this represents a decay to 'quantum equilibrium'. The proximity to equilibrium is characterized by the coarse-grained subquantum H-function which is found to decrease roughly exponentially towards zero over the course of time. The timescale tau for this relaxation is calculated for various values of M and the coarse-graining length epsilon. Its dependence on M is found to disagree with an earlier theoretical prediction. A power law - tau inversely proportional to M - is found to be fairly robust for all coarse-graining lengths and, although a weak dependence of tau on epsilon is observed, it does not appear to follow any straightforward scaling. A theoretical analysis is presented to explain these results. This improvement in our understanding of timescales for relaxation to quantum equilibrium is likely to be of use in the development of models of relaxation in the early universe, with a view to constraining possible violations of the Born rule in inflationary cosmology.Comment: 27 pages, 8 figures; Replacement with small number of changes reflecting referees' comment

Non-standard discretization of biological models

We consider certain types of discretization schemes for differential equations with quadratic nonlinearities, which were introduced by Kahan, and considered in a broader setting by Mickens. These methods have the property that they preserve important structural features of the original systems, such as the behaviour of solutions near to fixed points, and also, where appropriate (e.g. for certain mechanical systems), the property of being volume-preserving, or preserving a symplectic/Poisson structure. Here we focus on the application of Kahan's method to models of biological systems, in particular to reaction kinetics governed by the Law of Mass Action, and present a general approach to birational discretization, which is applied to population dynamics of Lotka-Volterra type

Benchmarking the performance of Density Functional Theory and Point Charge Force Fields in their Description of sI Methane Hydrate against Diffusion Monte Carlo

High quality reference data from diffusion Monte Carlo calculations are presented for bulk sI methane hydrate, a complex crystal exhibiting both hydrogen-bond and dispersion dominated interactions. The performance of some commonly used exchange-correlation functionals and all-atom point charge force fields is evaluated. Our results show that none of the exchange-correlation functionals tested are sufficient to describe both the energetics and the structure of methane hydrate accurately, whilst the point charge force fields perform badly in their description of the cohesive energy but fair well for the dissociation energetics. By comparing to ice Ih, we show that a good prediction of the volume and cohesive energies for the hydrate relies primarily on an accurate description of the hydrogen bonded water framework, but that to correctly predict stability of the hydrate with respect to dissociation to ice Ih and methane gas, accuracy in the water-methane interaction is also required. Our results highlight the difficulty that density functional theory faces in describing both the hydrogen bonded water framework and the dispersion bound methane.Comment: 8 pages, 4 figures, 1 table. Minor typos corrected and clarification added in Method

The alchemy of tendon repair: A primer for the (S)mad scientist

During vertebrate development, mesenchymal progenitors capable of forming bone, cartilage, muscle, fat, or tendon arise from either neural crest or somitic mesoderm. Transcriptional programs that specify mesenchymal cell fates are initiated and modified by paracrine cues provided by TGF-β superfamily members and mediated in part via the regulated assembly of Smad-containing multiprotein transcription factor complexes. In this issue of the JCI, Hoffmann and colleagues have identified that Smad8 activation drives tendon formation from C3H10T1/2 cells, a murine cell line that recapitulates many features of normal multipotent mesenchymal cells (see the related article beginning on page 940). Cells programmed to the tenocyte cell fate in vitro formed tenogenic grafts in vivo. These results add to the accumulating evidence that proliferating, multipotent mesenchymal progenitor cells can be programmed to yield multiple cell types — e.g., osteoblasts, myocytes, chondrocytes, and tenocytes — that may be useful in cell-based therapeutic approaches to musculoskeletal diseases