Interactions of age-dependent mortality and selectivity functions in age-based stock assessment models

The natural mortality rate (M) of fish varies with size and age, although it is often assumed to be constant in stock assessments. Misspecification of M may bias important assessment quantities. We simulated fishery data, using an age-based population model, and then conducted stock assessments on the simulated data. Results were compared to known values. Misspecification of M had a negligible effect on the estimation of relative stock depletion; however, misspecification of M had a large effect on the estimation of parameters describing the stock recruitment relationship, age-specific selectivity, and catchability. If high M occurs in juvenile and old fish, but is misspecified in the assessment model, virgin biomass and catchability are often poorly estimated. In addition, stock recruitment relationships are often very difficult to estimate, and steepness values are commonly estimated at the upper bound (1.0) and overfishing limits tend to be biased low. Natural mortality can be estimated in assessment models if M is constant across ages or if selectivity is asymptotic. However if M is higher in old fish and selectivity is dome-shaped, M and the selectivity cannot both be adequately estimated because of strong interactions between M and selectivity.

Ontogenetic patterns and temperature-dependent growth rates in early life stages of Pacific cod (Gadus macrocephalus)

Pacific cod (Gadus macrocephalus) is an important component of fisheries and food webs in the North Pacific Ocean and Bering Sea. However, vital rates of early life stages of this species have yet to be described in detail. We determined the thermal sensitivity of growth rates of embryos, preflexion and postflexion larvae, and postsettlement juveniles. Growth rates (length and mass) at each ontogenetic stage were measured in three replicate tanks at four to five temperatures. Nonlinear regression was used to obtain parameters for independent stage-specific growth functions and a unified size- and temperature-dependent growth function. Specific growth rates increased with temperature at all stages and generally decreased with increases in body size. However, these analyses revealed a departure from a strict size-based allometry in growth patterns, as reduced growth rates were observed among preflexion larvae: the reduction in specific growth rate between embryos and free-swimming larvae was greater than expected based on body size differences. Growth reductions in the preflexion larvae appear to be associated with increased metabolic rates and the transition from endogenous to exogenous feeding. In future studies, experiments should be integrated across life transitions to more clearly define intrinsic ontogenetic and size-dependent growth patterns because these are critical for evaluations of spatial and temporal variation in habitat quality.

Crank-Nicholson method for rate equations in powder random lasers

3rd International Conference on Mathematical Modeling in Physical Sciences (IC-MSQUARE 2014)

Estimating long-term growth-rate changes of southern bluefin tuna (Thunnus maccoyii) from two periods of tag-return data

Southern bluefin tuna (SBT) (Thunnus maccoyii) growth rates are estimated from tag-return data associated with two time periods, the 1960s and 1980s. The traditional von Bertalanffy growth model (VBG) and a two-phase VBG model were fitted to the data by maximum likelihood. The traditional VBG model did not provide an adequate representation of growth in SBT, and the two-phase VBG yielded a significantly better fit. The results indicated that significant change occurs in the pattern of growth in relation to a VBG curve during the juvenile stages of the SBT life cycle, which may be related to the transition from a tightly schooling fish that spends substantial time in near and surface shore waters to one that is found primarily in more offshore and deeper waters. The results suggest that more complex growth models should be considered for other tunas and for other species that show a marked change in habitat use with age. The likelihood surface for the two-phase VBG model was found to be bimodal and some implications of this are investigated. Significant and substantial differences were found in the growth for fish spawned in the 1960s and in the 1980s, such that after age four there is a difference of about one year in the expected age of a fish of similar length which persists over the size range for which meaningful recapture data are available. This difference may be a density-dependent response as a consequence of the marked reduction in the SBT population. Given the key role that estimates of growth have in most stock assessments, the results indicate that there is a need both for the regular monitoring of growth rates and for provisions for changes in growth over time (possibly related to changes in abundance) in the stock assessment models used for SBT and other species.

The influence of water-miscible solvents on the permeability of clay

Centrifuge tests were carried out to determine the effect of 5 different water-soluble chemicals on a thin consolidated disc of clay. The evolution of changes in the clay permeability with time was investigated and other structural changes due to chemical attack were monitored. The findings presented here demonstrate that the permeability of the clay appear to be generally related to the polarity of the chemicals and the dielectric constant, with the exception of Butanol. In the case of Butanol at low flow rate and low stress level, the action of the chemical caused the clay to crack, with a consequent large increase in flow.

Investigations on wooden floating materials: the loss of buoyancy under continuous immersion in water and the rate of its redemption by drying

A wooden fishing float under immersion in water for long periods is liable to absorb water, the quantity of water absorbed possibly being dependent upon the physical factors like the specific gravity and the inherent property of the material, the time of soaking and the pressure acting on it. Consequently a wooden float is likely to become heavy and loss its original buoyancy. However, when the float is removed from water and dried, the lost buoyancy is regained on complete drying. The present paper is an attempt to elucidate these two important characteristics of some of the chief wooden floating materials used on the West Coast of India.

Permeability and stiffness of sands at very low effective stresses

Loose saturated sandy soils may undergo liquefaction under cyclic loading, generating positive excess pore pressures due to their contractile nature and inability to dissipate pore pressures rapidly during earthquake loading. These liquefied soils have a near-zero effective stress state, and hence have very low strength and stiffness, causing severe damage to structures founded upon them. The duration for which this near-zero effective stress state persists is a function of the rate of reconsolidation of the liquefied soil, which in turn is a function of the permeability and stiffness of the soil at this very low effective stress. Existing literature based on observation of physical model tests suggests that the consolidation coefficient C v associated with this reconsolidation of liquefied sand is significantly lower than that of the same soil at moderate stress levels. In this paper, the results of a series of novel fluidisation tests in which permeability k and coefficient of consolidation C v were independently measured will be presented. These results allow calculation of the variation of stiffness E 0 and permeability k with effective stress. It is shown that while permeability increases markedly at very low effective stresses, the simultaneous drop in stiffness measured results in a decrease in consolidation coefficient and hence an increase in the duration for which the soil remains liquefied.

Spatial correlation of heat release rate and sound emission from turbulent premixed flames

The two-point spatial correlation of the rate of change of fluctuating heat release rate is central to the sound emission from open turbulent flames, and a few attempts have been made to address this correlation in recent studies. In this paper, the two-point correlation and its role in combustion noise are studied by analysing direct numerical simulation (DNS) data of statistically multi-dimensional turbulent premixed flames. The results suggest that this correlation function depends on the separation distance and direction but, not on the positions inside the flame brush. This correlation can be modelled using a combination of Hermite-Gaussian functions of zero and second order, i.e. functions of the form (1-Ax2)e-Bx2 for constants A and B, to include its possible negative values. The integral correlation volume obtained using this model is about 0.2δL3 with the length scale obtained from its cube root being about 0.6δ L, where δ L is the laminar flame thermal thickness. Both of the values are slightly larger than the values reported in an earlier study because of the anisotropy observed for the correlation. This model together with the turbulence-dependent parameter K, the ratio of the root-mean-square (RMS) value of the rate of change of reaction rate to the mean reaction rate, derived from the DNS data is applied to predict the far-field sound emitted from open flames. The calculated noise levels agree well with recently reported measurements and show a sensitivity to K values. © 2012 The Combustion Institute.

Measurement of filling-factor-dependent magnetophonon resonances in graphene using Raman spectroscopy

We perform polarization-resolved Raman spectroscopy on graphene in magnetic fields up to 45 T. This reveals a filling-factor-dependent, multicomponent anticrossing structure of the Raman G peak, resulting from magnetophonon resonances between magnetoexcitons and E2g phonons. This is explained with a model of Raman scattering taking into account the effects of spatially inhomogeneous carrier densities and strain. Random fluctuations of strain-induced pseudomagnetic fields lead to increased scattering intensity inside the anticrossing gap, consistent with the experiments. © 2013 American Physical Society.

Isolation, characterization and genome sequence of a birnavirus strain from flounder Paralichthys olivaceus in China

A birnavirus strain, Paralichthys olivaceus birnavirus (POBV), was isolated and characterized from cultured flounder in China, and its complete genomic sequence was subsequently determined. The virus could induce cytopathic effects (CPE) in four of seven fish cell lines and was resistant to chloroform, 5-iodo-2'-deoxyuridine, acid and alkaline pH, and heat treatment. Purified virus particles had a typical icosahedral shape, with a diameter of approximately 55-60 nm. The genomic segments A and B of POBV were 3,091 and 2,780 bp in length and shared many of the features of the members of the family Birnaviridae. Segment A contained two partially overlapping ORFs encoding a polyprotein, pVP2-VP4-VP3, and a nonstructural protein, VP5, while segment B had only one ORF encoding for the VP1, a viral RNA-dependent RNA polymerase (RdRp). This is the first report about a birnavirus strain from a new non-salmonid host in China and its complete genome sequence.

Microcystin-RR induced apoptosis in tobacco BY-2 suspension cells is mediated by reactive oxygen species and mitochondrial permeability transition pore status

When tobacco BY-2 cells were treated with 60 mu g/mL MC-RR for 5 d, time-dependent effects of MC-RR on the cells were observed. Morphological changes such as abnormal elongation, evident chromatin condensation and margination, fragmentation of nucleus and formation of apoptotic-like bodies suggest that 60 mu g/mL MC-RR induced rapid apoptosis in tobacco BY-2 cells. Moreover, there was a significant and rapid increase of ROS level before the loss of mitochondrial membrane potential (Delta Psi(m)) and the onset of cell apoptosis. Ascorbic acid (AsA), a major primary antioxidant, prevented the increase of ROS generation, blocked the decrease in Delta Psi(m) and subsequent cell apoptosis, indicating a critical role of ROS in serving as an important signaling molecule by causing a reduction of Delta Psi(m) and MC-RR-induced tobacco BY-2 cell apoptosis. In addition, a specific mitochondrial permeability transition pores (PTP) inhibitor, cyclosporin A (CsA), significantly blocked the MC-RR-induced ROS formation, loss of Delta Psi(m), as well as cell apoptosis when the cells were MC-RR stressed for 3 d, suggesting that PTP is involved in 60 mu g/mL MC-RR-induced tobacco cell apoptosis signalling process. Thus, we concluded that the mechanism of MC-RR-induced apoptosis signalling pathways in tobacco BY-2 cells involves not only the excess generation of ROS and oxidative stress, but also the opening of PTP inducing loss of mitochondrial membrane potential. (C) 2007 Published by Elsevier Ltd.

Dose-dependent effects of extracted microcystins on embryonic development, larval growth and histopathological changes of southern catfish (Silurus meridionalis)

A laboratory toxic experiment was conducted to examine dose-dependent effects of extracted microcystins (MCs) on embryonic development, larval growth and histopathological changes of southern catfish (Silurus meridionalis). Fertilized eggs were incubated in solutions with four concentrations of MCs (0, 1, 10, 100 mu g MC-LReq l(-1)). Higher MCs retarded egg development (2-10 h delays) and larval growth, reduced hatching rate (up to 45%), and caused high malformation rate (up to 15%) and hepatocytes damage (characterized by disorganization of cell structure and a loss of adherence between hepatocytes, cellular degeneration with vacuolar hepatocytes and marginal nuclei, even hepatocellular necrosis). A 10 mu g MC-LReql(-1) is close to a high concentration in natural cyanobacterial blooms, suggesting a possible existence of such toxic effects in eutrophic waters. (c) 2007 Elsevier Ltd. All rights reserved.

Construction and analysis of a high-CO2-requiring mutant of the cyanobacterium Anabaena sp strain PCC7120

A mutant of Anabaena sp. strain PCC7120 requiring high CO2 was generated using Tn5 mutagenesis. This is the first data for a filamentous cyanobacterium. The mutant was capable of growing at 5% CO2, but incapable of growing at air levels of CO2. Southern hybridization analysis indicated that the Anabaena genome was inserted by the transposon at one site. The apparent photosynthetic affinity of the mutant to external dissolved inorganic carbon (DIC) was about 300 times lower that of the wild type (WT), and the medium alkalization rate as well as the carboxysomal carbonic anhydrase activity of the mutant was also lower than those of the WT. When the mutant was transferred from the culture medium bubbled with 5% CO2 to higher DIC (8.4% CO2) or 1% CO2, it showed similar responses to the WT. However, aberrant carboxysomes were found in the mutant cells through ultrastructural analysis, indicating it was most probably the wrong organization of the carboxysomes that eventually led to the inefficient operation of carboxysomal carbonic anhydrase and the subsequent defectiveness of the mutant in utilizing DIC.

An inducible CO2 concentrating mechanism in cyanobacterium Anabaena sp strain PCC7120

In order to define its characteristics of the photosynthetic utilization of CO2 and HCO3- when the ambient inorganic carbon changed, HCG (High-CO2-Growing Cells) of cyanobacterium Anabaena sp. strain PCC7120 were prepared. The growth rate of HCG was higher than that of LCG (low-CO2-growing cells, i.e. air-growing cells). When the HCG cells were transferred from 5% CO2 to air levels of CO2 , a series of changes took place: its carbonic anhydrase activity as well as its photosynthetic affinity to the external inorganic carbon significantly increased; the number of the carboxysomes, which is one of the most important components of CCM in cyanobacteria also increased. These facts indicated that the CCM activity of Anabaena PCC 7120 was induced. When the pH in the medium increased from 6 to 9, the photosynthetic affinity to external inorganic carbon of both HCG and LCG declined, while the apparent photosynthetic affinity to external CO2 increased. In the light of these findings, this inducible CCM in cyanobacteria provided a good model for the study of the photosynthetic Ci utilization in the phototrophic microoganisms.

Effect of indium-doped interlayer on the strain relief in GaN films grown on Si(111)

Crack-free GaN films have been achieved by inserting an Indoped low-temperature (LT) AlGaN interlayer grown on silicon by metalorganic chemical vapor deposition. The relationship between lattice constants c and a obtained by X-ray diffraction analysis shows that indium doping interlayer can reduce the stress in GaN layers. The stress in GaN decreases with increasing trimethylindium (TMIn) during interlayer growth. Moreover, for a smaller TMIn flow, the stress in GaN decreases dramatically when In acts as a surfactant to improve the crystallinity of the AlGaN interlayer, and for a larger TMIn flow, the stress will increase again. The decreased stress leads to smoother surfaces and fewer cracks for GaN layers by using an In-doped interlayer than by using an undoped interlayer. In doping has been found to enhance the lateral growth and reduce the growth rate of the c face. It can explain the strain relief and cracks reduction in GaN films. (C) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.