Synthesizing and tuning chemical reaction networks with specified behaviours

We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First, we identify candidate CRNs that have the possibility to produce correct computations for a given finite set of inputs. We then optimise the reaction rates of each CRN using a combination of stochastic search techniques applied to the chemical master equation, simultaneously improving the of correct behaviour and ruling out spurious solutions. In addition, we use techniques from continuous time Markov chain theory to study the expected termination time for each CRN. We illustrate our approach by identifying CRNs for majority decision-making and division computation, which includes the identification of both known and unknown networks.Comment: 17 pages, 6 figures, appeared the proceedings of the 21st conference on DNA Computing and Molecular Programming, 201

Extragalactic Radio Continuum Surveys and the Transformation of Radio Astronomy

Next-generation radio surveys are about to transform radio astronomy by discovering and studying tens of millions of previously unknown radio sources. These surveys will provide new insights to understand the evolution of galaxies, measuring the evolution of the cosmic star formation rate, and rivalling traditional techniques in the measurement of fundamental cosmological parameters. By observing a new volume of observational parameter space, they are also likely to discover unexpected new phenomena. This review traces the evolution of extragalactic radio continuum surveys from the earliest days of radio astronomy to the present, and identifies the challenges that must be overcome to achieve this transformational change.Comment: To be published in Nature Astronomy 18 Sept 201

Quantifying the Detrimental Impacts of Land-Use and Management Change on European Forest Bird Populations

The ecological impacts of changing forest management practices in Europe are poorly understood despite European forests being highly managed. Furthermore, the effects of potential drivers of forest biodiversity decline are rarely considered in concert, thus limiting effective conservation or sustainable forest management. We present a trait-based framework that we use to assess the detrimental impact of multiple land-use and management changes in forests on bird populations across Europe. Major changes to forest habitats occurring in recent decades, and their impact on resource availability for birds were identified. Risk associated with these changes for 52 species of forest birds, defined as the proportion of each species' key resources detrimentally affected through changes in abundance and/or availability, was quantified and compared to their pan-European population growth rates between 1980 and 2009. Relationships between risk and population growth were found to be significantly negative, indicating that resource loss in European forests is an important driver of decline for both resident and migrant birds. Our results demonstrate that coarse quantification of resource use and ecological change can be valuable in understanding causes of biodiversity decline, and thus in informing conservation strategy and policy. Such an approach has good potential to be extended for predictive use in assessing the impact of possible future changes to forest management and to develop more precise indicators of forest health

Lorentz violation and Crab synchrotron emission: a new constraint far beyond the Planck scale

Special relativity asserts that physical phenomena appear the same for all inertially moving observers. This symmetry, called Lorentz symmetry, relates long wavelengths to short ones: if the symmetry is exact it implies that spacetime must look the same at all length scales. Several approaches to quantum gravity, however, suggest that there may be a Lorentz violating microscopic structure of spacetime, for example discreteness, non-commutativity, or extra dimensions. Here we determine a very strong constraint on a type of Lorentz violation that produces a maximum electron speed less than the speed of light. We use the observation of 100 MeV synchrotron radiation from the Crab nebula to improve the previous limits by a factor of 40 million, ruling out this type of Lorentz violation, and thereby providing an important constraint on theories of quantum gravity.Comment: 12 pages. Presentation shortened and revised for letter to Nature. New title "A strong astrophysical constraint on the violation of special relativity by quantum gravity". Maximum observed synchrotron frequency lowered, resulting in weakening the constraint from E_QG>4.5*10^27 GeV to E_QG>10^26 GeV. The role of the effective field theory assumptions underlying the analysis is highlighte

Geographic Variation of Strontium and Hydrogen Isotopes in Avian Tissue: Implications for Tracking Migration and Dispersal

Background: Isotopes can provide unique solutions to fundamental problems related to the ecology and evolution of migration and dispersal because prior movements of individuals can theoretically be tracked from tissues collected from a single capture. However, there is still remarkably little information available about how and why isotopes vary in wild animal tissues, especially over large spatial scales. Methodology/Principal Findings: Here, we describe variation in both stable-hydrogen (dDF) and strontium ( 87Sr/86SrF) isotopic compositions in the feathers of a migratory songbird, the Tree Swallow (Tachycineta bicolor), across 18 sampling sites in North America and then examine potential mechanisms driving this variation. We found that dDF was correlated with latitude of the sampling site, whereas 87Sr/86SrF was correlated with longitude. dDF was related to dD of meteoric waters where molting occurred and 87Sr/86SrF was influenced primarily by the geology in the area where feathers were grown. Using simulation models, we then assessed the utility of combining both markers to estimate the origin of individuals. Using 13 geographic regions, we found that the number of individuals correctly assigned to their site of origin increased from less than 40 % using either dD or 87Sr/86Sr alone to 74 % using both isotopes. Conclusions/Significance: Our results suggest that these isotopes have the potential to provide predictable an

Teachers as Educational Innovators in Inquiry-Based Science Teaching and Learning

This chapter describes inquiry-based science teaching and learning (IBST/L) pilots designed by teachers during a professional development programme. There is research-based evidence that IBSL/T may promote students’ learning and their motivation to learn science, and therefore it is beneficial to familiarise the teachers with this approach. Building on teachers’ existing expertise in designing their teaching, the programme introduced theoretical aspects of the IBST/L approach and its research-based benefits for students’ motivation, interest and science learning. The course aimed to support teachers as educational innovators in the process of designing and testing IBST/L pilots, during which they collaboratively reflected on and revised their existing practices. The data of this piece of research consists of the teachers’ poster presentations of their IBST/L pilots and a video recording of the reflection session. The content analysis revealed that the pilots’ structure seemed traditional but encompassed some IBST/L features. It is concluded that teacher educators need to understand teachers’ views of IBST/L in order to more effectively support planning and reflection.This chapter describes inquiry-based science teaching and learning (IBST/L) pilots designed by teachers during a professional development programme. There is research-based evidence that IBSL/T may promote students’ learning and their motivation to learn science, and therefore it is beneficial to familiarise the teachers with this approach. Building on teachers’ existing expertise in designing their teaching, the programme introduced theoretical aspects of the IBST/L approach and its research-based benefits for students’ motivation, interest and science learning. The course aimed to support teachers as educational innovators in the process of designing and testing IBST/L pilots, during which they collaboratively reflected on and revised their existing practices. The data of this piece of research consists of the teachers’ poster presentations of their IBST/L pilots and a video recording of the reflection session. The content analysis revealed that the pilots’ structure seemed traditional but encompassed some IBST/L features. It is concluded that teacher educators need to understand teachers’ views of IBST/L in order to more effectively support planning and reflection.Peer reviewe

Factors contributing to intervention fidelity in a multi-site chronic disease self-management program

BACKGROUND AND OBJECTIVES: Disease self-management programs have been a popular approach to reducing morbidity and mortality from chronic disease. Replicating an evidence-based disease management program successfully requires practitioners to ensure fidelity to the original program design. METHODS: The Florida Health Literacy Study (FHLS) was conducted to investigate the implementation impact of the Pfizer, Inc. Diabetes Mellitus and Hypertension Disease Self-Management Program based on health literacy principles in 14 community health centers in Florida. The intervention components discussed include health educator recruitment and training, patient recruitment, class sessions, utilization of program materials, translation of program manuals, patient retention and follow-up, and technical assistance. RESULTS: This report describes challenges associated with achieving a balance between adaptation for cultural relevance and fidelity when implementing the health education program across clinic sites. This balance was necessary to achieve effectiveness of the disease self-management program. The FHLS program was implemented with a high degree of fidelity to the original design and used original program materials. Adaptations identified as advantageous to program participation are discussed, such as implementing alternate methods for recruiting patients and developing staff incentives for participation. CONCLUSION: Effective program implementation depends on the talent, skill and willing participation of clinic staff. Program adaptations that conserve staff time and resources and recognize their contribution can increase program effectiveness without jeopardizing its fidelity

Nitrogen fixation and transfer in open ocean diatom–cyanobacterial symbioses

Many diatoms that inhabit low-nutrient waters of the open ocean live in close association with cyanobacteria. Some of these associations are believed to be mutualistic, where N2-fixing cyanobacterial symbionts provide N for the diatoms. Rates of N2 fixation by symbiotic cyanobacteria and the N transfer to their diatom partners were measured using a high-resolution nanometer scale secondary ion mass spectrometry approach in natural populations. Cell-specific rates of N2 fixation (1.15–71.5 fmol N per cell h−1) were similar amongst the symbioses and rapid transfer (within 30 min) of fixed N was also measured. Similar growth rates for the diatoms and their symbionts were determined and the symbiotic growth rates were higher than those estimated for free-living cells. The N2 fixation rates estimated for Richelia and Calothrix symbionts were 171–420 times higher when the cells were symbiotic compared with the rates estimated for the cells living freely. When combined, the latter two results suggest that the diatom partners influence the growth and metabolism of their cyanobacterial symbionts. We estimated that Richelia fix 81–744% more N than needed for their own growth and up to 97.3% of the fixed N is transferred to the diatom partners. This study provides new information on the mechanisms controlling N input into the open ocean by symbiotic microorganisms, which are widespread and important for oceanic primary production. Further, this is the first demonstration of N transfer from an N2 fixer to a unicellular partner. These symbioses are important models for molecular regulation and nutrient exchange in symbiotic systems

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets