On board sampling of the rockfish and lingcod commerical passenger fishing vessel industry in northern and central California, May 1987 to December 1991

From May 1987 to June 1990 and from August to December 1991 Fishery Technicians sampled catches on board 690 Commercial Passenger Fishing Vessel (CPFV) trips targeting rockfish and lingcod from the general port areas of Fort Bragg, Bodega Bay, San Francisco, Monterey, and Morro Bay. Data are presented for species composition by port area, year, and month, for catch-per-unit-effort, mean length, and length frequency of lingcod and the 18 most frequently observed rockfish species, and for trends in fishing effort related to fishing time, depth, and distance from port. Total catch estimates are presented based on unadjusted logbook records, logbook records adjusted by sampling data and compliance rates, and effort data from a marine recreational fishing statistics survey. Average catch of kept fish per angler day was 11.8 and average catch of kept fish per angler hour was 3.7. A trend of an increasing frequency of trips to deep (>40 fm) locations was observed in the Bodega Bay, San Francisco, and Monterey areas from 1988 to 1990-91. No trend was evident relative to trip frequency and distance from port. A total of 74 species was observed caught during the study. Rockfishes comprised 88.5% to 97.9% by number of the observed catch by port area. The five most frequently observed species were chilipepper, blue, yellowtail, and widow rockfishes, and bocaccio, with lingcod ranking seventh. In general, mean length and catch-per-angler-hour of sport fishes caught by CPFV anglers varied considerably and did not show steady declines during the study period. However, port-specific areas of major concern were identified for chilipepper, lingcod, and black rockfish, and to a lesser extent brown, canary, vermilion, yelloweye, olive, and widow rockfish. These areas of concern included steadily declining catch rate, steadily declining mean length, and a high percentage of sexually immature fish in the sampled-catch. Recent sampling of the commercial hook-and-line fishery in northern and central California indicated that most species of rockfishes taken by CPFV anglers are also harvested commercially. (261pp.

A general framework for integrating environmental time series into stock assessment models: model description, simulation testing, and example

We present a method to integrate environmental time series into stock assessment models and to test the significance of correlations between population processes and the environmental time series. Parameters that relate the environmental time series to population processes are included in the stock assessment model, and likelihood ratio tests are used to determine if the parameters improve the fit to the data significantly. Two approaches are considered to integrate the environmental relationship. In the environmental model, the population dynamics process (e.g. recruitment) is proportional to the environmental variable, whereas in the environmental model with process error it is proportional to the environmental variable, but the model allows an additional temporal variation (process error) constrained by a log-normal distribution. The methods are tested by using simulation analysis and compared to the traditional method of correlating model estimates with environmental variables outside the estimation procedure. In the traditional method, the estimates of recruitment were provided by a model that allowed the recruitment only to have a temporal variation constrained by a log-normal distribution. We illustrate the methods by applying them to test the statistical significance of the correlation between sea-surface temperature (SST) and recruitment to the snapper (Pagrus auratus) stock in the Hauraki Gulf–Bay of Plenty, New Zealand. Simulation analyses indicated that the integrated approach with additional process error is superior to the traditional method of correlating model estimates with environmental variables outside the estimation procedure. The results suggest that, for the snapper stock, recruitment is positively correlated with SST at the time of spawning

Sequential CCR5-Tropic HIV-1 Reactivation from Distinct Cellular Reservoirs following Perturbation of Elite Control

Background HIV Elite Controllers may reveal insights into virus persistence given they harbour small reservoir sizes, akin to HIV non-controllers treated early with combination antiretroviral therapy. Both groups of patients represent the most promising candidates for interventions aimed at sustained remission or ‘cure’. Analytic treatment interruption (ATI) in the latter group leads to stochastic rebound of virus, though it is unclear whether loss of elite control is also associated with similar rebound characteristics. Methods We studied three discrete periods of virus rebound during myeloma related immune disruption over 2.5 years in an elite controller who previously underwent autologous stem cell transplantation (ASCT) in the absence of any antiretroviral therapy. Single genome sequencing of the V1-V4 region of env in PBMC and plasma was performed and phylogenies reconstructed. Average pairwise distance (APD) was calculated and non-parametric methods used to assess compartmentalisation. Coreceptor usage was predicted based on genotypic algorithms. Results 122 single genome sequences were obtained (median 26 sequences per rebound). The initial rebounding plasma env sequences following ASCT represented two distinct lineages, and clustered with proviral DNA sequences isolated prior to ASCT. One of the lineages was monophyletic, possibly indicating reactivation from clonally expanded cells. The second rebound occurred 470 days after spontaneous control of the first rebound and was phylogenetically distinct from the first, confirmed by compartmentalisation analysis, with a different cellular origin rather than ongoing replication. By contrast, third rebound viruses clustered with second rebound viruses, with evidence for ongoing evolution that was associated with lymphopenia and myeloma progression. Following ASCT a shift in tropism from CXCR4-tropic viruses to a CCR5-tropic population was observed to persist through to the third rebound. Conclusions Our data highlight similarities in the viral reservoir between elite and non-controllers undergoing ATI following allogeneic transplantation. The lack of propagation of CXCR4 using viruses following transplantation warrants further study

Using airborne LiDAR Survey to explore historic-era archaeological landscapes of Montserrat in the eastern Caribbean

This article describes what appears to be the first archaeological application of airborne LiDAR survey to historic-era landscapes in the Caribbean archipelago, on the island of Montserrat. LiDAR is proving invaluable in extending the reach of traditional pedestrian survey into less favorable areas, such as those covered by dense neotropical forest and by ashfall from the past two decades of active eruptions by the Soufrière Hills volcano, and to sites in localities that are inaccessible on account of volcanic dangers. Emphasis is placed on two aspects of the research: first, the importance of ongoing, real-time interaction between the LiDAR analyst and the archaeological team in the field; and second, the advantages of exploiting the full potential of the three-dimensional LiDAR point cloud data for purposes of the visualization of archaeological sites and features

Kin selection, quorum sensing and virulence in pathogenic bacteria

Bacterial growth and virulence often depends upon the cooperative release of extracellular factors excreted in response to quorum sensing (QS).We carried out an in vivo selection experiment in mice to examine how QS evolves in response to variation in relatedness (strain diversity), and the consequences for virulence. We started our experiment with two bacterial strains: a wild-type that both produces and responds to QS signal molecules, and a lasR (signal-blind) mutant that does not release extracellular factors in response to signal. We found that: (i) QS leads to greater growth within hosts; (ii) high relatedness favours the QS wild-type; and (iii) low relatedness favours the lasR mutant. Relatedness matters in our experiment because, at relatively low relatedness, the lasR mutant is able to exploit the extracellular factors produced by the cells that respond to QS, and hence increase in frequency. Furthermore, our results suggest that because a higher relatedness favours cooperative QS, and hence leads to higher growth, this will also lead to a higher virulence, giving a relationship between relatedness and virulence that is in the opposite direction to that usually predicted by virulence theory

A Comparison of quality of life outcomes following different techniques of mastoid surgery

- Background: Mastoid surgery carried out to treat chronic otitis media (COM) can lead to an improvement in objective and subjective measures post-operatively. This study aims to look at the subjective change in quality of life using the Glasgow Benefit Inventory relative to the type of mastoid surgery undertaken. - Method: A retrospective multi-centre postal questionnaire survey of 157 patients who underwent mastoid surgery from 2008-2012. - Results: 83 questionnaire responses were received from patients having the surgery at 3 different hospitals (a response rate of 53%). 57% of patients had a Glasgow benefit Score of 0 indicating no change in quality of life post-operatively. 35% scored +50 indicating a significant improvement. The only significant difference found was that women fare worse after surgery than men. - Conclusions: The choice of mastoid surgery technique should be determined by clinical need and surgeon preference. There is no improvement in quality of life for most patients

Pulsar Timing with the Parkes Radio Telescope for the Fermi Mission

We report here on two years of timing of 168 pulsars using the Parkes radio telescope. The vast majority of these pulsars have spin-down luminosities in excess of 10^34 erg/s and are prime target candidates to be detected in gamma-rays by the Fermi Gamma-Ray Space Telescope. We provide the ephemerides for the ten pulsars being timed at Parkes which have been detected by Fermi in its first year of operation. These ephemerides, in conjunction with the publicly available photon list, can be used to generate gamma-ray profiles from the Fermi archive. We will make the ephemerides of any pulsars of interest available to the community upon request. In addition to the timing ephemerides, we present the parameters for 14 glitches which have occurred in 13 pulsars, seven of which have no previously known glitch history. The Parkes timing programme, in conjunction with Fermi observations, is expected to continue for at least the next four years.Comment: Accepted for publication in PASA.12 page

A Minimal Model of Signaling Network Elucidates Cell-to-Cell Stochastic Variability in Apoptosis

Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The structure of this minimal network is derived based on some simple assumptions on its differential response to external stimuli. We employ stochastic differential equations and probability distributions obtained from stochastic simulations to characterize differential signaling response in our minimal network model. We show that the proposed minimal signaling network displays two distinct types of response as the strength of the stimulus is decreased. The signaling network has a deterministic part that undergoes rapid activation by a strong stimulus in which case cell-to-cell fluctuations can be ignored. As the strength of the stimulus decreases, the stochastic part of the network begins dominating the signaling response where slow activation is observed with characteristic large cell-to-cell stochastic variability. Interestingly, this proposed stochastic signaling network can capture some of the essential signaling behaviors of a complex apoptotic cell death signaling network that has been studied through experiments and large-scale computer simulations. Thus we claim that the proposed signaling network is an appropriate minimal model of apoptosis signaling. Elucidating the fundamental design principles of complex cellular signaling pathways such as apoptosis signaling remains a challenging task. We demonstrate how our proposed minimal model can help elucidate the effect of a specific apoptotic inhibitor Bcl-2 on apoptotic signaling in a cell-type independent manner. We also discuss the implications of our study in elucidating the adaptive strategy of cell death signaling pathways.Comment: 9 pages, 6 figure

The prevalence of vitamin B12 deficiency in a random sample from the Australian population

 Objective: Vitamin B12 deficiency is common in older adults, and may increase the risk of cognitive impairment. The distribution of vitamin B12 insufficiency in younger age groups is less studied. This study aims to assess the prevalence of vitamin B12 deficiency (<156ρmol/L) and subclinical low-normal levels (156-250ρmol/L) in a large, random sample of the Australian population across the adult life span. Methods: We examined serum vitamin B12 levels in a random sample of 1,085 men and 1,125 women aged 20-97 years between 1994 and 2006; in the Barwon Statistical Division, a regional area in south eastern Australia that is representative of the socioeconomic status of the Australian population. Results: The age-standardised prevalence of vitamin B12 deficiency in this cohort of men and women was 3.6%. Subclinical low-normal vitamin B12 levels (156-250ρmol/L) were found in 26%. Serum vitamin B12 levels declined with age among men (p-value <0.001) and were lower in men than women (p-value <0.001). Vitamin B12 levels were higher among supplement users (8.0% of the cohort). Conclusions: Vitamin B12 levels decline with age, and have been associated with neurodegenerative diseases and cognitive decline. Early intervention by diet education or supplement use to address this age-associated decline in vitamin levels may be an effective strategy to prevent decline in a significant segment of the population. Such intervention may need to start in mid-life (from 50-years of age) before the onset age-related decline in vitamin B12 levels