Inference by Minimizing Size, Divergence, or their Sum

We speed up marginal inference by ignoring factors that do not significantly contribute to overall accuracy. In order to pick a suitable subset of factors to ignore, we propose three schemes: minimizing the number of model factors under a bound on the KL divergence between pruned and full models; minimizing the KL divergence under a bound on factor count; and minimizing the weighted sum of KL divergence and factor count. All three problems are solved using an approximation of the KL divergence than can be calculated in terms of marginals computed on a simple seed graph. Applied to synthetic image denoising and to three different types of NLP parsing models, this technique performs marginal inference up to 11 times faster than loopy BP, with graph sizes reduced up to 98%-at comparable error in marginals and parsing accuracy. We also show that minimizing the weighted sum of divergence and size is substantially faster than minimizing either of the other objectives based on the approximation to divergence presented here.Comment: Appears in Proceedings of the Twenty-Sixth Conference on Uncertainty in Artificial Intelligence (UAI2010

Andersen-Tawil Syndrome

Andersen-Tawil syndrome (ATS) is a rare condition consisting of ventricular arrhythmias, periodic paralysis, and dysmorphic features. In 2001, mutations in KCNJ2, which encodes the α subunit of the potassium channel Kir2.1, were identified in patients with ATS. To date, KCNJ2 is the only gene implicated in ATS, accounting for approximately 60% of cases. ATS is a unique channelopathy, and represents the first link between cardiac and skeletal muscle excitability. The arrhythmias observed in ATS are distinctive; patients may be asymptomatic, or minimally symptomatic despite a high arrhythmia burden with frequent ventricular ectopy and bidirectional ventricular tachycardia. However, patients remain at risk for life-threatening arrhythmias, including torsades de pointes and ventricular fibrillation, albeit less commonly than observed in other genetic arrhythmia syndromes. The characteristic heterogeneity at both the genotypic and phenotypic levels contribute to the continued difficulties with appropriate diagnosis, risk stratification, and effective therapy. The initial recognition of a syndromic association of clinically diverse symptoms, and the subsequent identification of the underlying molecular genetic basis of ATS has enhanced both clinical care, and our understanding of the critical function of Kir2.1 on skeletal muscle excitability and cardiac action potentia

Rubisco evolution in C4 eudicots: an analysis of Amaranthaceae sensu lato

BACKGROUND Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots. METHODOLOGY/PRINCIPAL FINDINGS We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution. CONCLUSIONS/SIGNIFICANCE Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.This research was funded by NERC (http://www.nerc.ac.uk/; grant number NE/H007741/1)

Mammals of the Mixedwood Plains Ecozone

Ontario and Quebec were totally covered with ice during the last glaciation. Deglaciation was followed by gradual post-glacial repopulation of these two provinces (and others) by mammals from source areas in the United States. Thus most range expansions were from south to north east of the Great Lakes. The mammalian fauna of the Mixedwood Plains Ecozone has been steadily changing since deglaciation about 10 000 years ago. During this period a succession of species assemblages has moved through this ecozone as the climate warmed. Several of the larger mammal species known from this area became extinct during this period of change. These included giant beavers, woolly mammoths, mastodons and species of deer and bison (Harington, 1989). Throughout this period there have been steady, gradual changes in the biodiversity of the Mixedwood Plains Ecozone, but the most rapid changes have occurred over the last 300 years. The best sources of information on the ranges of the mammals of the Ontario and Quebec parts of this ecozone are Peterson (1966) for both parts; Dobbyn (1994) and Peterson (1957) for Ontario; and Prescott and Richard (1982) for Quebec. Currently in the Mixedwood Plains Ecozone there are about 59 species of mammals in 44 genera and 16 families. This does not include four species recorded in this ecozone, but not established as part of its mammal fauna. An Evening Bat (Nycticeius humeralis) accidently occurred in the Lake Erie Lowland Ecoregion once. Black Rats (Rattus rattus), Coypus (Myocaster coypus), and Domestic Ferrets (Mustela putorius) have all been introduced but have not persisted. Although the species richness of mammals has increased since European settlement, biodiversity has decreased in the Mixedwood Plains Ecozone through the reduction in population size of many ecologically important species and the complete disappearance of others. Wolverines, Cougars and Wapiti have all been extirpated from this ecozone. Many species of mammals have been extirpated from much of their former ranges in this ecozone because of destruction of forest habitat, over-harvesting of pelts by fur trappers, over-hunting, and persecution of predators. Southwestern Ontario is an area of special concern because of the permanent conversion of most forests to agricultural land; this has resulted in a dramatic decrease in mammalian biodiversity. The loss of some native species has been coupled with increases in several new species through range expansion or direct introduction from other ecozones. The new species are typically generalists that have adapted to living in disturbed habitats. Our knowledge of the status of mammal populations in the Mixedwood Plains Ecozone is nowhere near complete. The status and complete distribution are known for only a few species monitored today because of their economic importance. The status of a few other species has been examined by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC); its status designations will be mentioned later in the species accounts. Monitoring programs should be established to determine the status of ecologically important species for proper biodiversity assessments of this ecozone. Many small mammals such as shrews, moles, bats, squirrels, mice, and voles could easily be monitored with existing techniques. Larger mammals would be more difficult to monitor but there are effective methods available. Large mammalian predator populations should be monitored as indicators of ecosystem health. Historically in the Mixedwood Plains Ecozone predator populations have declined most dramatically because of human disturbances

Modelling the Fluid Mechanics of Cilia and Flagella in Reproduction and Development

Cilia and flagella are actively bending slender organelles, performing functions such as motility, feeding and embryonic symmetry breaking. We review the mechanics of viscous-dominated microscale flow, including time-reversal symmetry, drag anisotropy of slender bodies, and wall effects. We focus on the fundamental force singularity, higher order multipoles, and the method of images, providing physical insight and forming a basis for computational approaches. Two biological problems are then considered in more detail: (1) left-right symmetry breaking flow in the node, a microscopic structure in developing vertebrate embryos, and (2) motility of microswimmers through non-Newtonian fluids. Our model of the embryonic node reveals how particle transport associated with morphogenesis is modulated by the gradual emergence of cilium posterior tilt. Our model of swimming makes use of force distributions within a body-conforming finite element framework, allowing the solution of nonlinear inertialess Carreau flow. We find that a three-sphere model swimmer and a model sperm are similarly affected by shear-thinning; in both cases swimming due to a prescribed beat is enhanced by shear-thinning, with optimal Deborah number around 0.8. The sperm exhibits an almost perfect linear relationship between velocity and the logarithm of the ratio of zero to infinite shear viscosity, with shear-thickening hindering cell progress.Comment: 20 pages, 24 figure

Multiscale probability mapping: groups, clusters and an algorithmic search for filaments in SDSS

We have developed a multiscale structure identification algorithm for the detection of overdensities in galaxy data that identifies structures having radii within a user-defined range. Our "multiscale probability mapping" technique combines density estimation with a shape statistic to identify local peaks in the density field. This technique takes advantage of a user-defined range of scale sizes, which are used in constructing a coarse-grained map of the underlying fine-grained galaxy distribution, from which overdense structures are then identified. In this study we have compiled a catalogue of groups and clusters at 0.025 < z < 0.24 based on the Sloan Digital Sky Survey, Data Release 7, quantifying their significance and comparing with other catalogues. Most measured velocity dispersions for these structures lie between 50 and 400 km/s. A clear trend of increasing velocity dispersion with radius from 0.2 to 1 Mpc/h is detected, confirming the lack of a sharp division between groups and clusters. A method for quantifying elongation is also developed to measure the elongation of group and cluster environments. By using our group and cluster catalogue as a coarse-grained representation of the galaxy distribution for structure sizes of <~ 1 Mpc/h, we identify 53 filaments (from an algorithmically-derived set of 100 candidates) as elongated unions of groups and clusters at 0.025 < z < 0.13. These filaments have morphologies that are consistent with previous samples studied.Comment: 22 pages, 14 figures and 6 tables. Accepted for publication in MNRAS. Data products, three-dimensional visualisations and further information about MSPM can be found at http://www.physics.usyd.edu.au/sifa/Main/MSPM/ . v2 contains two additional references. v3 has a slightly altered title and updated reference