Online discovery of similarity mappings

We consider the problem of choosing, sequentially, a map which assigns elements of a set A to a few elements of a set B. On each round, the algorithm suffers some cost associated with the chosen assignment, and the goal is to minimize the cumulative loss of these choices relative to the best map on the entire sequence. Even though the offline problem of finding the best map is provably hard, we show that there is an equivalent online approximation algorithm, Randomized Map Prediction (RMP), that is efficient and performs nearly as well. While drawing upon results from the "Online Prediction with Expert Advice" setting, we show how RMP can be utilized as an online approach to several standard batch problems. We apply RMP to online clustering as well as online feature selection and, surprisingly, RMP often outperforms the standard batch algorithms on these problems.

Persistent ocean monitoring with underwater gliders : adapting sampling resolution

Ocean processes are dynamic, complex, and occur on multiple spatial and temporal scales. To obtain a synoptic view of such processes, ocean scientists collect data over long time periods. Historically, measurements were continually provided by fixed sensors, e.g., moorings, or gathered from ships. Recently, an increase in the utilization of autonomous underwater vehicles has enabled a more dynamic data acquisition approach. However, we still do not utilize the full capabilities of these vehicles. Here we present algorithms that produce persistent monitoring missions for underwater vehicles by balancing path following accuracy and sampling resolution for a given region of interest, which addresses a pressing need among ocean scientists to efficiently and effectively collect high-value data. More specifically, this paper proposes a path planning algorithm and a speed control algorithm for underwater gliders, which together give informative trajectories for the glider to persistently monitor a patch of ocean. We optimize a cost function that blends two competing factors: maximize the information value along the path, while minimizing deviation from the planned path due to ocean currents. Speed is controlled along the planned path by adjusting the pitch angle of the underwater glider, so that higher resolution samples are collected in areas of higher information value. The resulting paths are closed circuits that can be repeatedly traversed to collect long-term ocean data in dynamic environments. The algorithms were tested during sea trials on an underwater glider operating off the coast of southern California, as well as in Monterey Bay, California. The experimental results show significant improvements in data resolution and path reliability compared to previously executed sampling paths used in the respective regions.

A crystallographic snapshot of tyrosine trans-phosphorylation in action

Tyrosine trans-phosphorylation is a key event in receptor tyrosine kinase signaling, yet, the structural basis for this process has eluded definition. Here, we present the crystal structure of the FGF receptor 2 kinases caught in the act of trans-phosphorylation of Y769, the major C-terminal phosphorylation site. The structure reveals that enzyme- and substrate-acting kinases engage each other through elaborate and specific interactions not only in the immediate vicinity of Y769 and the enzyme active site, but also in regions that are as much of 18 A away from D626, the catalytic base in the enzyme active site. These interactions lead to an unprecedented level of specificity and precision during the trans-phosphorylation on Y769. Time-resolved mass spectrometry analysis supports the observed mechanism of trans-phosphorylation. Our data provide a molecular framework for understanding the mechanism of action of Kallmann syndrome mutations and the order of trans-phosphorylation reactions in FGFRs. We propose that the salient mechanistic features of Y769 trans-phosphorylation are applicable to trans-phosphorylation of the equivalent major phosphorylation sites in many other RTKs.

Relationship between physical activity and stiff or painful joints in mid-aged women and older women: a 3-year prospective study

This prospective study examined the association between physical activity and the incidence of self-reported stiff or painful joints (SPJ) among mid-age women and older women over a 3-year period. Data were collected from cohorts of mid-age (48–55 years at Time 1; n = 4,780) and older women (72–79 years at Time 1; n = 3,970) who completed mailed surveys 3 years apart for the Australian Longitudinal Study on Women's Health. Physical activity was measured with the Active Australia questions and categorized based on metabolic equivalent value minutes per week: none (<40 MET.min/week); very low (40 to <300 MET.min/week); low (300 to <600 MET.min/week); moderate (600 to <1,200 MET.min/week); and high (1,200+ MET.min/week). Cohort-specific logistic regression models were used to examine the association between physical activity at Time 1 and SPJ 'sometimes or often' and separately 'often' at Time 2. Respondents reporting SPJ 'sometimes or often' at Time 1 were excluded from analysis. In univariate models, the odds of reporting SPJ 'sometimes or often' were lower for mid-age respondents reporting low (odds ratio (OR) = 0.77, 95% confidence interval (CI) = 0.63–0.94), moderate (OR = 0.82, 95% CI = 0.68–0.99), and high (OR = 0.75, 95% CI = 0.62–0.90) physical activity levels and for older respondents who were moderately (OR = 0.80, 95% CI = 0.65–0.98) or highly active (OR = 0.83, 95% CI = 0.69–0.99) than for those who were sedentary. After adjustment for confounders, these associations were no longer statistically significant. The odds of reporting SPJ 'often' were lower for mid-age respondents who were moderately active (OR = 0.71, 95% CI = 0.52–0.97) than for sedentary respondents in univariate but not adjusted models. Older women in the low (OR = 0.72, 95% CI = 0.55–0.96), moderate (OR = 0.54, 95% CI = 0.39–0.76), and high (OR = 0.61, 95% CI = 0.46–0.82) physical activity categories had lower odds of reporting SPJ 'often' at Time 2 than their sedentary counterparts, even after adjustment for confounders. These results are the first to show a dose–response relationship between physical activity and arthritis symptoms in older women. They suggest that advice for older women not currently experiencing SPJ should routinely include counseling on the importance of physical activity for preventing the onset of these symptoms.

A compact interferometric sensor design using three waveguide coupling

The use of metal stripes for the guiding of plasmons is a well established technique for the infrared regime and has resulted in the development of a myriad of passive optical components and sensing devices. However, the plasmons suffer from large losses around sharp bends, making the compact design of nanoscale sensors and circuits problematic. A compact alternative would be to use evanescent coupling between two sufficiently close stripes, and thus we propose a compact interferometer design using evanescent coupling. The sensitivity of the design is compared with that achieved using a hand-held sensor based on the Kretschmann style surface plasmon resonance technique. Modeling of the new interferometric sensor is performed for various structural parameters using finite-difference time-domain and COMSOL Multiphysics. The physical mechanisms behind the coupling and propagation of plasmons in this structure are explained in terms of the allowed modes in each section of the device.

Right to the city, desire for the suburb?

The 2000s have been a lively decade for cities. The Worldwatch Institute estimated that 2007 was the first year in human history that more people worldwide lived in cities than the countryside. Globalisation and new digital media technologies have generated the seemingly paradoxical outcome that spatial location came to be more rather than less important, as combinations of firms, industries, cultural activities and creative talents have increasingly clustered around a select node of what have been termed “creative cities,” that are in turn highly networked into global circuits of economic capital, political power and entertainment media. Intellectually, the period has seen what the UCLA geographer Ed Soja refers to as the spatial turn in social theory, where “whatever your interests may be, they can be significantly advanced by adopting a critical spatial perspective”. This is related to the dynamic properties of socially constructed space itself, or what Soja terms “the powerful forces that arise from socially produced spaces such as urban agglomerations and cohesive regional economies,” with the result that “what can be called the stimulus of socio-spatial agglomeration is today being assertively described as the primary cause of economic development, technological innovation, and cultural creativity”

Stochastic simulation for spatial modelling of dynamic process in a living cell

One of the fundamental motivations underlying computational cell biology is to gain insight into the complicated dynamical processes taking place, for example, on the plasma membrane or in the cytosol of a cell. These processes are often so complicated that purely temporal mathematical models cannot adequately capture the complex chemical kinetics and transport processes of, for example, proteins or vesicles. On the other hand, spatial models such as Monte Carlo approaches can have very large computational overheads. This chapter gives an overview of the state of the art in the development of stochastic simulation techniques for the spatial modelling of dynamic processes in a living cell.

Simulations of the effect of waveguide cross-section on quantum dot – plasmon coupling

Quantum dot - plasmon waveguide systems are of interest for the active control of plasmon propagation, and consequently, the development of active nanophotonic devices such as nano-sized optical transistors. This paper is concerned with how varying aspect ratio of the waveguide crosssection affects the quantum dot - plasmon coupling. We compare a stripe waveguide with an equivalent nanowire, illustrating that both waveguides have a similar coupling strength to a nearby quantum dot for small waveguide cross-section, thereby indicating that stripe lithographic waveguides have strong potential use in quantum dot –plasmon waveguide systems. We also demonstrate that changing the aspect ratio of both stripe and wire waveguides can increase the spontaneous emission rate of the quantum dot into the plasmon mode, by up to a factor of five. The results of this paper will contribute to the optimisation of quantum dot - plasmon waveguide systems and help pave the way for the development of active nanophotonics devices.

Knowledge and attitudes of paediatric nurses related to breastfeeding

Introduction: Almost 90% of Australian mothers are exclusively breastfeeding when they discharge from maternity hospitals but by six months of age breastfeeding infants have reduced to 32% nationally and 19% in Queensland, far below the national target of 80%. Many factors influence the choice to breastfeed, including health care provision, therefore the knowledge and attitudes of paediatric nurses have the potential to affect breastfeeding duration. Aims: To assess current breastfeeding knowledge and attitudes of paediatric nurses in metropolitan and regional Queensland settings. Method: The study used a cross-sectional survey design. The tool was developed from several documented health professional questionnaires about breastfeeding, with permission from authors. Survey items relating breastfeeding physiology, factors relating to breastfeeding success, and local, national and international policies were also included. Ethics approval was granted from the appropriate Ethics Committees to conduct the survey through tertiary metropolitan and regional hospital settings. Results: A total of 241 surveys were returned, achieving a response rate of 53%. Nurses acknowledged breastmilk as the best source of nutrition for infants (99%, n=238) and that mothers should be encouraged to breastfeed (92%, n=221). However, many respondents considered infant formula a nutritional equivalent (44%, n=105) and (47%, n=113) were unaware that supplemental formulas interfered with successful breastfeeding. Most nurses recognised that stress (e.g. infant hospitalisation) impacts on the success of breastfeeding (90%, n=216). Knowledge of breastfeeding anatomy and physiology was poor and a substantial number of nurses did not identify correct attachment in response to two diagrammatic representations (76%, n=183 and 45%, n=109). Survey results demonstrated deficiencies in knowledge that would impact on support provided to breastfeeding mothers. Knowledge deficits were also identified relating to local, national and international policies and protocols concerning breastfeeding and breastmilk substitutes. Conclusion: Breastfeeding knowledge and attitudes were exceptional in areas related to general breastfeeding knowledge. However, in areas directly related to nursing practice, considerable deficits in paediatric nurses' knowledge and attitudes were identified. Lack of appropriate skills, knowledge and varying attitudes amongst paediatric nurses has the potential to negatively impact on the education, advice and support provided to breastfeeding mothers and their families whilst their infant is in hospital. These study findings will guide future research and strategies to improve knowledge and policy statements to assist paediatric nurses in fulfilling their role.

Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Sequestration through forestry and agriculture

Current climate mitigation policies have not fully resolved contentious issues regarding the inclusion of carbon sequestration through changes in forestry and agricultural management practices. Terrestrial carbon sinks could be a low-cost mitigation option that fosters conservation and development, yet issues related to accurately documenting the amount of carbon sequestered undermine confidence that emission offsets through sequestration are equivalent to emission reductions. From an atmospheric perspective, net of CO2 removals through sequestration are equivalent to emission reductions over a given period of time. But carbon will not remain sequestered in biomass or soils indefinitely and investments in sequestration could stifle investments in reducing emissions from other sources. Many international climate agreements cap emissions from some countries or sectors but enable participation of uncapped countries or sectors for forestry and agricultural sequestration. This structure can prompt emission increases in parts of the uncapped entities that weaken the value of emission reductions earned through sequestration. This has been a minor issue under the Clean Development Mechanism of the Kyoto Protocol. Reduced emissions through deforestation and degradation is susceptible to the same problems. The purpose of this article is to review the science, politics, and policy that form the basis of arguments for and against the inclusion forestry and agricultural sequestration as a component of current and future international climate mitigation policies.

The undirected feedback vertex set problem has a Poly(k) Kernel

Resolving a noted open problem, we show that the Undirected Feedback Vertex Set problem, parameterized by the size of the solution set of vertices, is in the parameterized complexity class Poly(k), that is, polynomial-time pre-processing is sufficient to reduce an initial problem instance (G, k) to a decision-equivalent simplified instance (G', k') where k' � k, and the number of vertices of G' is bounded by a polynomial function of k. Our main result shows an O(k11) kernelization bound.

Least-squares congealing for large numbers of images

In this paper we pursue the task of aligning an ensemble of images in an unsupervised manner. This task has been commonly referred to as “congealing” in literature. A form of congealing, using a least-squares criteria, has been recently demonstrated to have desirable properties over conventional congealing. Least-squares congealing can be viewed as an extension of the Lucas & Kanade (LK)image alignment algorithm. It is well understood that the alignment performance for the LK algorithm, when aligning a single image with another, is theoretically and empirically equivalent for additive and compositional warps. In this paper we: (i) demonstrate that this equivalence does not hold for the extended case of congealing, (ii) characterize the inherent drawbacks associated with least-squares congealing when dealing with large numbers of images, and (iii) propose a novel method for circumventing these limitations through the application of an inverse-compositional strategy that maintains the attractive properties of the original method while being able to handle very large numbers of images.

Ocular characteristics in myopic anisometropia

PURPOSE: To investigate the interocular symmetry of ocular optical, biometric and biomechanical characteristics between the more and less ametropic eyes of myopic anisometropes. METHODS: Thirty-four young, healthy myopic anisometropic adults (≥ 1 D spherical equivalent difference between eyes) without amblyopia or strabismus were recruited. A range of biometric and optical parameters were measured in the more and less ametropic eye of each subject including; axial length, ocular aberrations, intraocular pressure and corneal topography, thickness and biomechanics. Morphology of the anterior eye in primary and downward gaze was examined using custom software analysis of high resolution digital images. Ocular sighting dominance was assessed using the hole-in-the-card test. RESULTS: Mean absolute spherical equivalent anisometropia was 1.74 ± 0.74 D. There was a strong correlation between the degree of anisometropia and the interocular difference in axial length (r = 0.81, p < 0.001). The more and less ametropic fellow eyes displayed a high degree of interocular symmetry for the majority of biometric, biomechanical and optical parameters measured. When the level of anisometropia exceeded 1.75 D (n = 10), the more myopic eye was the dominant sighting eye in nine of these ten subjects. Subjects with greater levels of anisometropia (> 1.75 D) also showed high levels of correlation between the dominant and non-dominant eyes in their biometric, biomechanical and optical characteristics. CONCLUSIONS: Although significantly different in axial length, anisometropic eyes display a high degree of interocular symmetry for a range of anterior eye biometrics and optical parameters. For higher levels of anisometropia, the more myopic eye tends to be the dominant sighting eye.