Temporal trends in reef fish assemblages inside Virgin Islands National Park and around St. John, U.S. Virgin Islands, 1988-2006

This report is a result of long-term fish monitoring studies supported by the National Park Service (NPS) at the Virgin Islands National Park since 1988 and is now a joint NPS and NOAA collaboration. Reef fish monitoring data collected from 1988 to 2006 within Virgin Islands National Park (VINP) and adjacent reefs around St. John, U.S. Virgin Islands (USVI) were analyzed to provide information on the status of reef fishes during the monitoring period. Monitoring projects were initiated by the National Park Service (NPS) in the 1980s to provide useful data for evaluation of resources and for development of a long-term monitoring program. Monthly monitoring was conducted at two reef sites (Yawzi Point and Cocoloba Cay) starting in November 1988 for 2.5 years to document the monthly/seasonal variability in reef fish assemblages. Hurricane Hugo (a powerful Category 4 storm) struck the USVI in September 1989 resulting in considerable damage to the reefs around St. John. Abundance of fishes was lower at both sites following the storm, however, a greater effect was observed at Yawzi Point, which experienced a more direct impact from the hurricane. The storm affected species differently, with some showing only small, short-term declines in abundance, and others, such as the numerically abundant blue chromis (Chromis cyanea), a planktivorous damselfish, exhibiting a larger and longer recovery period. This report provides: 1) an evaluation of sampling methods, sample size, and methods used during the sampling period, 2) an evaluation of the spatial and temporal variability in reef fish assemblages at selected reef sites inside and outside of VINP, and 3) an evaluation of trends over 17 years of monitoring at the four reference sites. Comparisons of methods were conducted to standardize assessments among years. Several methods were used to evaluate sample size requirements for reef fish monitoring and the results provided a statistically robust justification for sample allocation.

Mission report: a strategy to inventory, characterize, and monitor the marine region within and around the National Park and Monument boundaries of St. John, USVI, July 21- July 31, 2008

The intent of this field mission was to continue ongoing efforts: (1) to spatially characterize and monitor the distribution, abundance and size of both reef fishes and conch within and around the waters of the Virgin Islands National Park (VIIS) and newly established Virgin Islands Coral Reef National Monument (VICR), (2) to correlate this information to in-situ data collected on associated habitat parameters, (3) to use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting and to establish the efficacy of those management decisions. This work is supported by the National Park Service and NOAA’s Coral Reef Conservation Program’s Caribbean Coral Reef Ecosystem Monitoring Project. The report highlights the successes of this mission.

The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha)

We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988–98 to examine the spatial and temporal basis of population structure in the watershed. Genetically discrete chinook salmon populations were associated with almost all spawning sites, although gene flow within some tributaries prevented or limited differentiation among spawning groups. The mean FST value over 52 samples and 13 loci surveyed was 0.039. Geographic structuring of populations was apparent: distinct groups were identified in the upper, middle, and lower Fraser River regions, and the north, south, and lower Thompson River regions. The geographically and temporally isolated Birkenhead River population of the lower Fraser region was sufficiently genetically distinctive to be treated as a separate region in a hierarchial analysis of gene diversity. Approximately 95% of genetic variation was contained within populations, and the remainder was accounted for by differentiation among regions (3.1%), among populations within regions (1.3%), and among years within populations (0.5%).Analysis of allelic diversity and private alleles did not support the suggestion that genetically distinctive populations of chinook salmon in the south Thompson were the result of postglacial hybridization of ocean-type and stream-type chinook in the Fraser River drainage. However, the relatively small amount of differentiation among Fraser River chinook salmon populations supports the suggestion that gene flow among genetically distinct groups of postglacial colonizing groups of chinook salmon has occurred, possibly prior to colonization of the Fraser River drainage.

Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha)

Variation at 13 microsatellite loci was previously surveyed in approximately 7400 chinook salmon (Oncorhynchus tshawytscha) sampled from 50 localities in the Fraser River drainage in southern British Columbia. Evaluation of the utility of the microsatellite variation for population-specific stock identification applications indicated that the accuracy of the stock composition estimates generally improved with an increasing number of loci used in the estimation procedure, but an increase in accuracy was generally marginal after eight loci were used. With 10–14 populations in a simulated fishery sample, the mean error in population-specific estimated stock composition with a 50-popula-tion baseline was <1.4%. Identification of individuals to specific populations was highest for lower Fraser River and lower and North Thompson River populations; an average of 70% of the individual fish were correctly assigned to specific populations. The average error of the estimated percentage for the seven populations present in a coded-wire tag sample was 2% per population. Estimation of stock composition in the lower river commercial net fishery prior to June is of key local fishery management interest. Chinook salmon from the Chilcotin River and Nicola River drainages were important contributors to the early commercial fishery in the lower river because they comprised approximately 50% of the samples from the net fishery prior to mid April.

Age and growth of the smooth dogfish (Mustelus canis) in the northwest Atlantic Ocean

The northwest Atlantic population of smooth dogfish (Mustelus canis) ranges from Cape Cod, Massachusetts, to South Carolina. Although M. canis is seasonally abundant in this region, very little is known about important aspects of its biology, such as growth and reproductive rates. In the early 1990s, commercial fishery landings of smooth dogfish dramatically increased on the east coast of the United States. This study investigated growth rates of the east coast M. canis population through analysis of growth patterns in vertebral centra. Marginal increment analysis, estimates of precision, and patterns in seasonal growth supported the use of vertebrae to age these sharks. Growth bands in vertebral samples were used to estimate ages for 894 smooth dogfish. Age-length data were used to determine von Bertalanffy growth parameters for this population: K = 0.292/yr, L∞ = 123.57 cm, and t0 = –1.94 years for females, and K = 0.440/yr, L∞ = 105.17 cm, and t0 = –1.52 years for males. Males matured at two or three years of age and females matured between four and seven years of age. The oldest age estimate for male and female samples was ten and sixteen years, respectively.

Modelling of long-term ground response to tunnelling under St James's Park, London

Following a tunnel excavation in low-permeability soil, it is commonly observed that the ground surface continues to settle and ground loading on the tunnel lining changes, as the pore pressures in the ground approach a new equilibrium condition. The monitored ground response following the tunnelling under St James's Park, London, shows that the mechanism of subsurface deformation is composed of three different zones: swelling, consolidation and rigid body movement. The swelling took place in a confined zone above the tunnel crown, extending vertically to approximately 5 m above it. On the sides of the tunnel, the consolidation of the soil occurred in the zone primarily within the tunnel horizon, from the shoulder to just beneath the invert, and extending laterally to a large offset from the tunnel centreline. Above these swelling and consolidation zones the soil moved downward as a rigid body. In this study, soil-fluid coupled three-dimensional finite element analyses were performed to simulate the mechanism of long-term ground response monitored at St James's Park. An advanced critical state soil model, which can simulate the behaviour of London Clay in both drained and undrained conditions, was adopted for the analyses. The analysis results are discussed and compared with the field monitoring data. It is found that the observed mechanism of long-term subsurface ground and tunnel lining response at St James's Park can be simulated accurately only when stiffness anisotropy, the variation of permeability between different units within the London Clay and non-uniform drainage conditions for the tunnel lining are considered. This has important implications for future prediction of the long-term behaviour of tunnels in clays.

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

Numerical simulation of long-term twin-tunnel behaviour at St James's park

The twin-tunnel construction of the Jubilee Line Extension tunnels beneath St James's Park was simulated using coupled-consolidation finite-element analyses. The effect of defining different permeabilities for the final consolidation stage was investigated, and the performance of a fissure softening model was also evaluated. The analyses suggested an unexpectedly high permeability anisotropy for soil around the tunnel crown, possibly due to stress-induced permeability changes, or low-permeability laminations. Also, the permeability profile and lining conductivity were found to differ between the tunnels. Inclusion of the fissure model gave a narrower settlement trough, more alike that in the field, by preferentially softening simple shear behaviour. Long-term settlements at the site continue to increase at an unexpectedly high rate, suggesting the possibility of creep or unexpected soil softening during excavation. © 2012 Taylor & Francis Group.

Ocean urea fertilization for carbon credits poses high ecological risks

The proposed plan for enrichment of the Sulu Sea, Philippines, a region of rich marine biodiversity, with thousands of tonnes of urea in order to stimulate algal blooms and sequester carbon is flawed for multiple reasons. Urea is preferentially used as a nitrogen source by some cyanobacteria and dinoflagellates, many of which are neutrally or positively buoyant. Biological pumps to the deep sea are classically leaky, and the inefficient burial of new biomass makes the estimation of a net loss of carbon from the atmosphere questionable at best. The potential for growth of toxic dinoflagellates is also high, as many grow well on urea and some even increase their toxicity when grown on urea. Many toxic dinoflagellates form cysts which can settle to the sediment and germinate in subsequent years, forming new blooms even without further fertilization. If large-scale blooms do occur, it is likely that they will contribute to hypoxia in the bottom waters upon decomposition. Lastly, urea production requires fossil fuel usage, further limiting the potential for net carbon sequestration. The environmental and economic impacts are potentially great and need to be rigorously assessed. (C) 2008 Elsevier Ltd. All rights reserved.

Taxi! Urban economies and the social and transport Impacts of the taxicab.

The taxicab provides a significant contribution to the accessibility of a city and provides a wide range of services across many social groups. Considering the role of the taxi this books examines the impacts that the mode currently has, and how it may continue to develop in the provision of access within the city.

Development of process control methodology for tracking the quality and safety of pain, agitation and sedation management in critical care units

Objective: To develop sedation, pain, and agitation quality measures using process control methodology and evaluate their properties in clinical practice. Design: A Sedation Quality Assessment Tool was developed and validated to capture data for 12-hour periods of nursing care. Domains included pain/discomfort and sedation-agitation behaviors; sedative, analgesic, and neuromuscular blocking drug administration; ventilation status; and conditions potentially justifying deep sedation. Predefined sedation-related adverse events were recorded daily. Using an iterative process, algorithms were developed to describe the proportion of care periods with poor limb relaxation, poor ventilator synchronization, unnecessary deep sedation, agitation, and an overall optimum sedation metric. Proportion charts described processes over time (2 monthly intervals) for each ICU. The numbers of patients treated between sedation-related adverse events were described with G charts. Automated algorithms generated charts for 12 months of sequential data. Mean values for each process were calculated, and variation within and between ICUs explored qualitatively. Setting: Eight Scottish ICUs over a 12-month period. Patients: Mechanically ventilated patients. Interventions: None. Measurements and Main Results: The Sedation Quality Assessment Tool agitation-sedation domains correlated with the Richmond Sedation Agitation Scale score (Spearman [rho] = 0.75) and were reliable in clinician-clinician (weighted kappa; [kappa] = 0.66) and clinician-researcher ([kappa] = 0.82) comparisons. The limb movement domain had fair correlation with Behavioral Pain Scale ([rho] = 0.24) and was reliable in clinician-clinician ([kappa] = 0.58) and clinician-researcher ([kappa] = 0.45) comparisons. Ventilator synchronization correlated with Behavioral Pain Scale ([rho] = 0.54), and reliability in clinician-clinician ([kappa] = 0.29) and clinician-researcher ([kappa] = 0.42) comparisons was fair-moderate. Eight hundred twenty-five patients were enrolled (range, 59-235 across ICUs), providing 12,385 care periods for evaluation (range 655-3,481 across ICUs). The mean proportion of care periods with each quality metric varied between ICUs: excessive sedation 12-38%; agitation 4-17%; poor relaxation 13-21%; poor ventilator synchronization 8-17%; and overall optimum sedation 45-70%. Mean adverse event intervals ranged from 1.5 to 10.3 patients treated. The quality measures appeared relatively stable during the observation period. Conclusions: Process control methodology can be used to simultaneously monitor multiple aspects of pain-sedation-agitation management within ICUs. Variation within and between ICUs could be used as triggers to explore practice variation, improve quality, and monitor this over time

Robotic grasping by showing: an experimental comparison of two novel algorithms.

Neal M J, Boyce D, Rowland J J, Lee M H, and Olivier P L. Robotic grasping by showing: an experimental comparison of two novel algorithms. In Proceedings of IFAC - SICICA'97, pages 345-350, Annecy, France, 1997.

Teaching by Example in Food Assembly by Robot

T. G. Williams, J.J. Rowland, Lee M.H. and M.J. Neal Teaching by Example in Food Assembly by Robot, Proc. 2000 IEEE Int. Conf. On Robotics and Automation, San Francisco, April 2000, pp3247-52.