Polynomial Method for PLL Controller Optimization†

The Phase-Locked Loop (PLL) is a key component of modern electronic communication and control systems. PLL is designed to extract signals from transmission channels. It plays an important role in systems where it is required to estimate the phase of a received signal, such as carrier tracking from global positioning system satellites. In order to robustly provide centimeter-level accuracy, it is crucial for the PLL to estimate the instantaneous phase of an incoming signal which is usually buried in random noise or some type of interference. This paper presents an approach that utilizes the recent development in the semi-definite programming and sum-of-squares field. A Lyapunov function will be searched as the certificate of the pull-in range of the PLL system. Moreover, a polynomial design procedure is proposed to further refine the controller parameters for system response away from the equilibrium point. Several simulation results as well as an experiment result are provided to show the effectiveness of this approach

Drivers and predictions of coral reef carbonate budget trajectories

The largest threat to the long-term existent of coral reefs is climate change, and this topic has received much attention over the past 20 years as coral bleaching and mortality events have become more frequent and more intense. As a result of these events, changes in different aspects of coral reef ecosystems have potentially changed the balance of carbonate accretion and erosion. These geomorphic consequences of coral bleaching have yet to received significant attention, with most studies being conducted on reef ecology, and here we begin to rectify this omission. Using data collected on inner Seychelles reefs from 1994 to 2014 we track the carbonate budget of these reefs across the 1998 coral bleaching event when 90% of coral cover was lost, and subsequent recovery. We found that while all reefs were estimated have positive budgets, and thus were accreting in 1994, in 2005 almost all reefs were in an erosional (negative budget) state. By 2014, 7 reefs had recovered to positive carbonate budgets. However, where macroalgae was previously found, and was now dominant, carbonate budgets remained negative. Boosted regression tree models indicated that reefs with higher massive coral, low macroalgae cover and low biomass of excavating parrotfishes in 1994 were more likely to recover by 2014. However, in 2016 a second bleaching-induced mass-mortality of corals occurred. If this mortality is similar to 1998, we predict that six of eight reefs that had positive budgets in 2014 would recover to positive budgets again by 2030. However, no currently negative budget reef would recover. Our results highlighted that coral reef framework maintenance potential should not be assumed from ecological state, and that management has a role to play in promoting resilient carbonate accretion on coral reefs

Computerized ICU Data Management Pitfalls and Promises

journal articleBiomedical Informatic

Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago

Turnip mosaic potyvirus (TuMV) is probably the most widespread and damaging virus that infects cultivated brassicas worldwide. Previous work has indicated that the virus originated in western Eurasia, with all of its closest relatives being viruses of monocotyledonous plants. Here we report that we have identified a sister lineage of TuMV-like potyviruses (TuMV-OM) from European orchids. The isolates of TuMV-OM form a monophyletic sister lineage to the brassica-infecting TuMVs (TuMV-BIs), and are nested within a clade of monocotyledon-infecting viruses. Extensive host-range tests showed that all of the TuMV-OMs are biologically similar to, but distinct from, TuMV-BIs and do not readily infect brassicas. We conclude that it is more likely that TuMV evolved from a TuMV-OM-like ancestor than the reverse. We did Bayesian coalescent analyses using a combination of novel and published sequence data from four TuMV genes [helper component-proteinase protein (HC-Pro), protein 3(P3), nuclear inclusion b protein (NIb), and coat protein (CP)]. Three genes (HC-Pro, P3, and NIb), but not the CP gene, gave results indicating that the TuMV-BI viruses diverged from TuMV-OMs around 1000 years ago. Only 150 years later, the four lineages of the present global population of TuMV-BIs diverged from one another. These dates are congruent with historical records of the spread of agriculture in Western Europe. From about 1200 years ago, there was a warming of the climate, and agriculture and the human population of the region greatly increased. Farming replaced woodlands, fostering viruses and aphid vectors that could invade the crops, which included several brassica cultivars and weeds. Later, starting 500 years ago, inter-continental maritime trade probably spread the TuMV-BIs to the remainder of the world

A broad distribution of the alternative oxidase in microsporidian parasites

Microsporidia are a group of obligate intracellular parasitic eukaryotes that were considered to be amitochondriate until the recent discovery of highly reduced mitochondrial organelles called mitosomes. Analysis of the complete genome of Encephalitozoon cuniculi revealed a highly reduced set of proteins in the organelle, mostly related to the assembly of ironsulphur clusters. Oxidative phosphorylation and the Krebs cycle proteins were absent, in keeping with the notion that the microsporidia and their mitosomes are anaerobic, as is the case for other mitosome bearing eukaryotes, such as Giardia. Here we provide evidence opening the possibility that mitosomes in a number of microsporidian lineages are not completely anaerobic. Specifically, we have identified and characterized a gene encoding the alternative oxidase (AOX), a typically mitochondrial terminal oxidase in eukaryotes, in the genomes of several distantly related microsporidian species, even though this gene is absent from the complete genome of E. cuniculi. In order to confirm that these genes encode functional proteins, AOX genes from both A. locustae and T. hominis were over-expressed in E. coli and AOX activity measured spectrophotometrically using ubiquinol-1 (UQ-1) as substrate. Both A. locustae and T. hominis AOX proteins reduced UQ-1 in a cyanide and antimycin-resistant manner that was sensitive to ascofuranone, a potent inhibitor of the trypanosomal AOX. The physiological role of AOX microsporidia may be to reoxidise reducing equivalents produced by glycolysis, in a manner comparable to that observed in trypanosome

Explaining the persistence of low income and environmentally degrading land uses in the Brazilian Amazon

Tropical forests continue to be plagued by the dual sustainability challenges of deforestation and rural poverty. We seek to understand why many of the farmers living in the Brazilian Amazon, home to the world’s largest tropical agricultural-forest frontier, persist in agricultural activities associated with low incomes and high environmental damage. To answer this question, we assess the factors that shape the development and distribution of agricultural activities and farmer well-being in these frontiers. Our study utilizes a uniquely comprehensive social-ecological dataset from two regions in the eastern Brazilian Amazon and employs a novel conceptual framework that highlights the interdependencies between household attributes, agricultural activities, and well-being. We find that livestock production, which yields the lowest per hectare incomes, remains the most prevalent land use in remote areas, but many examples of high income fruit, horticulture, and staple crop production exist on small properties, particularly in peri-urban areas. The transition to more profitable land uses is limited by lagging supply chain infrastructure, social preferences, and the fact that income associated with land use activities is not a primary source of perceived life quality. Instead subjective well-being is more heavily influenced by the nonmonetary attributes of a rural lifestyle (safety, tranquility, community relations, etc.). We conclude that transitions away from low-income land uses in agricultural-forest frontiers of the Brazilian Amazon need not abandon a land-focused vision of development, but will require policies and programs that identify and discriminate households based on a broader set of household assets, cultural attributes, and aspirations than are traditionally applied. At a broader scale, access to distant markets for high value crops must be improved via investments in processing, storage, and marketing infrastructure

The SNAPSHOT study protocol : SNAcking, Physical activity, Self-regulation, and Heart rate Over Time

Peer reviewedPublisher PD

Climate warming, marine protected areas and the ocean-scale integrity of coral reef ecosystems

Coral reefs have emerged as one of the ecosystems most vulnerable to climate variation and change. While the contribution of a warming climate to the loss of live coral cover has been well documented across large spatial and temporal scales, the associated effects on fish have not. Here, we respond to recent and repeated calls to assess the importance of local management in conserving coral reefs in the context of global climate change. Such information is important, as coral reef fish assemblages are the most species dense vertebrate communities on earth, contributing critical ecosystem functions and providing crucial ecosystem services to human societies in tropical countries. Our assessment of the impacts of the 1998 mass bleaching event on coral cover, reef structural complexity, and reef associated fishes spans 7 countries, 66 sites and 26 degrees of latitude in the Indian Ocean. Using Bayesian meta-analysis we show that changes in the size structure, diversity and trophic composition of the reef fish community have followed coral declines. Although the ocean scale integrity of these coral reef ecosystems has been lost, it is positive to see the effects are spatially variable at multiple scales, with impacts and vulnerability affected by geography but not management regime. Existing no-take marine protected areas still support high biomass of fish, however they had no positive affect on the ecosystem response to large-scale disturbance. This suggests a need for future conservation and management efforts to identify and protect regional refugia, which should be integrated into existing management frameworks and combined with policies to improve system-wide resilience to climate variation and change