Indexed induction and coinduction, fibrationally.

This paper extends the fibrational approach to induction and coinduction pioneered by Hermida and Jacobs, and developed by the current authors, in two key directions. First, we present a sound coinduction rule for any data type arising as the final coalgebra of a functor, thus relaxing Hermida and Jacobs’ restriction to polynomial data types. For this we introduce the notion of a quotient category with equality (QCE), which both abstracts the standard notion of a fibration of relations constructed from a given fibration, and plays a role in the theory of coinduction dual to that of a comprehension category with unit (CCU) in the theory of induction. Second, we show that indexed inductive and coinductive types also admit sound induction and coinduction rules. Indexed data types often arise as initial algebras and final coalgebras of functors on slice categories, so our key technical results give sufficent conditions under which we can construct, from a CCU (QCE) U : E -> B, a fibration with base B/I that models indexing by I and is also a CCU (QCE)

Radioisotopes and coastal research in the Great Barrier Reef

Radioisotopes are efficient tracers of coastal processes on various spatial and temporal scales. The isotopes of radon and radium are particularly useful tools to understand hydrological land-ocean interaction because (a) activities of these isotopes are elevated in groundwater by two to three orders of magnitude in comparison with seawater, and (b) these isotopes have half-lives similar to the time scales of coastal hydrological processes such as river and groundwater discharge to the ocean, as well as coastal ocean mixing (or residence) time. The application of these isotopes to studies of land-ocean interaction in the central Great Barrier Reef region (Townsville to Cooktown) is illustrated in three recent studies: (1) coastal mapping of radon on a regional scale improves the understanding of the spatial variability of river and groundwater fluxes to the Great Barrier Reef lagoon; (2) quantification of tidal water exchange between mangrove forests and creeks demonstrates the significant contributions this process makes to water flux and associated geochemical fluxes along tropical coastlines; (3) estimates of coastal water residence time contribute to the understanding of the fate of land-derived solutes in the Great Barrier Reef Lagoon. Concurrent mapping of 222Rn (half-life 3.8 days) and salinity allows an efficient qualitative assessment of land–ocean interaction on various spatial and temporal scales. From shore-parallel transects along the Central Great Barrier Reef coastline with a surface-towed and continuously recording multi-detector system, numerous locations of elevated radon activities can be identified as terrestrially-derived submarine groundwater discharge, riverine sources, and the recirculation of seawater through crustacean burrows in mangrove forests. Variations in the inverse relationship of 222Rn and salinity in different tropical wet seasons reveal ‘timing’ aspects of large-scale freshwater input during the tropical wet season into the lagoon. Subsequently, 222Rn was used together with radium isotopes to quantify the tidal water exchange between a mangrove forest on Hinchinbrook Island and the ocean. Significant export of these radio-nuclides from the forest into a tidal creek indicates continuous tidally-driven circulation through animal burrows in the forest. The forest floor is efficiently flushed, with water flux of about 30 L m-2 day-1 of forest floor, which is equivalent to about 10% of the total burrow volume in the forest per tidal cycle. This work illustrates the physical process which supports export of organic and inorganic matter from mangrove forests to the coastal zone. Importantly, annual average circulation fluxes through mangrove forest floors are of the same order as annual river discharge in the central GBR. Finally, an improved understanding of the fate of land-derived waters is of great importance to current discussions about water quality management in the Great Barrier Reef. The mixing of coastal waters is an important parameter influencing the health of these ecosystems. Time constants associated with the decay of four naturally-occurring isotopes of radium span large time scales; 224Ra, 223Ra, 228Ra and 226Ra have half-lives of 4 days, 11 days, 6 years and 1620 years respectively. The radium quartet has been used to determine time scales of mixing of near-shore water and deep ocean water. This study demonstrates that central GBR water within 20 km of the coast is flushed with outer lagoon water on a timescale of 18–45 days, with the flushing time increasing northward. This difference likely reflects the different reef matrix density in the two zones, affecting exchange with offshore Coral Sea water

Synthesis of accelerograms compatible with the Chinese GB 50011-2001 design spectrum via harmonic wavelets: artificial and historic records

A versatile approach is employed to generate artificial accelerograms which satisfy the compatibility criteria prescribed by the Chinese aseismic code provisions GB 50011-2001. In particular, a frequency dependent peak factor derived by means of appropriate Monte Carlo analyses is introduced to relate the GB 50011-2001 design spectrum to a parametrically defined evolutionary power spectrum (EPS). Special attention is given to the definition of the frequency content of the EPS in order to accommodate the mathematical form of the aforementioned design spectrum. Further, a one-to-one relationship is established between the parameter controlling the time-varying intensity of the EPS and the effective strong ground motion duration. Subsequently, an efficient auto-regressive moving-average (ARMA) filtering technique is utilized to generate ensembles of non-stationary artificial accelerograms whose average response spectrum is in a close agreement with the considered design spectrum. Furthermore, a harmonic wavelet based iterative scheme is adopted to modify these artificial signals so that a close matching of the signals’ response spectra with the GB 50011-2001 design spectrum is achieved on an individual basis. This is also done for field recorded accelerograms pertaining to the May, 2008 Wenchuan seismic event. In the process, zero-phase high-pass filtering is performed to accomplish proper baseline correction of the acquired spectrum compatible artificial and field accelerograms. Numerical results are given in a tabulated format to expedite their use in practice

Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms

The main functions of viral capsids are to protect, transport and deliver their genome. The mechanical properties of capsids are supposed to be adapted to these tasks. Bacteriophage capsids also need to withstand the high pressures the DNA is exerting onto it as a result of the DNA packaging and its consequent confinement within the capsid. It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. DNA packaging and ejection strategies are obviously dependent on the mechanical properties of the capsid. This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular

Burden and risk factors for Pseudomonas aeruginosa community-acquired pneumonia:a Multinational Point Prevalence Study of Hospitalised Patients

Pseudornonas aeruginosa is a challenging bacterium to treat due to its intrinsic resistance to the antibiotics used most frequently in patients with community-acquired pneumonia (CAP). Data about the global burden and risk factors associated with P. aeruginosa-CAP are limited. We assessed the multinational burden and specific risk factors associated with P. aeruginosa-CAP. We enrolled 3193 patients in 54 countries with confirmed diagnosis of CAP who underwent microbiological testing at admission. Prevalence was calculated according to the identification of P. aeruginosa. Logistic regression analysis was used to identify risk factors for antibiotic-susceptible and antibiotic-resistant P. aeruginosa-CAP. The prevalence of P. aeruginosa and antibiotic-resistant P. aeruginosa-CAP was 4.2% and 2.0%, respectively. The rate of P. aeruginosa CAP in patients with prior infection/colonisation due to P. aeruginosa and at least one of the three independently associated chronic lung diseases (i.e. tracheostomy, bronchiectasis and/or very severe chronic obstructive pulmonary disease) was 67%. In contrast, the rate of P. aeruginosa-CAP was 2% in patients without prior P. aeruginosa infection/colonisation and none of the selected chronic lung diseases. The multinational prevalence of P. aeruginosa-CAP is low. The risk factors identified in this study may guide healthcare professionals in deciding empirical antibiotic coverage for CAP patients

Development of a core descriptor set for Crohn's anal fistula

AIM: Crohn's anal fistula (CAF) is a complex condition, with no agreement on which patient characteristics should be routinely reported in studies. The aim of this study was to develop a core descriptor set of key patient characteristics for reporting in all CAF research. METHOD: Candidate descriptors were generated from published literature and stakeholder suggestions. Colorectal surgeons, gastroenterologists and specialist nurses in inflammatory bowel disease took part in three rounds of an international modified Delphi process using nine-point Likert scales to rank the importance of descriptors. Feedback was provided between rounds to allow refinement of the next ratings. Patterns in descriptor voting were assessed using principal component analysis (PCA). Resulting PCA groups were used to organize items in rounds two and three. Consensus descriptors were submitted to a patient panel for feedback. Items meeting predetermined thresholds were included in the final set and ratified at the consensus meeting. RESULTS: One hundred and thirty three respondents from 22 countries completed round one, of whom 67.0% completed round three. Ninety seven descriptors were rated across three rounds in 11 PCA-based groups. Forty descriptors were shortlisted. The consensus meeting ratified a core descriptor set of 37 descriptors within six domains: fistula anatomy, current disease activity and phenotype, risk factors, medical interventions for CAF, surgical interventions for CAF, and patient symptoms and impact on quality of life. CONCLUSION: The core descriptor set proposed for all future CAF research reflects characteristics important to gastroenterologists and surgeons. This might aid transparent reporting in future studies