Limiting inter-annual variation in total allowable catch strategies. An application to ICES roundfish stocks

This study evaluated through simulation management strategy that stabilise catch levels by setting bounds on the inter-annual variability in Total Allowable Catches (TACs). An integrated modelling approach was used, which modelled both the ‘real’ and observed systems and the interactions between all system components. The modelling framework therefore allowed evaluation of the robustness of candidate management strategies to both the intrinsic properties of the systems, and the ability to observe, monitor, assess and control them. Strategies were evaluated in terms of level of risk (measured as the probability of spawning stock biomass falling below the biomass limit reference level for the stock) and cumulative yield. The simulation approach used provides a powerful tool for the examination of the performance of candidate management strategies. It has shown that better management is not necessarily going to be achieved by improving the assessement, since even with a perfect assessment (where the simulated working group knew stock status perfectly) stocks may crash at fishing levels that standard stochastic projections would suggest were safe. Also explicitly modelling the assessment process can result in quite different outcomes than those predicted by the simple projection traditionally used by stock assessment working groups. This is because the simple projection assumes that the status of the stock in the current year is known without error and that the target fishing mortality can be achieved without error. However, in practice the assessment is based on last years data and the effect of any management measure on SSB is only manifest, following the implementation of the quota, at the end of the following year. The choice of target and fishing mortality levels and minimum stock levels results from ICES interpretation of the precautionary approach. This lead to the definition of fishing mortality and biomass reference points that are intended to prevent over-fishing and to trigger recovery plans when a stock is overfished respectively. Although, fishing mortality and biomass reference points were originally intended to be independent, a fishing mortality level implies a corresponding biomass level. In the case of saithe a fishing mortality of 0.40 (i.e. the FPA level) would drive the stock to Blim, suggesting that the choice of biomass and target reference points are not consistent for this stock

Limiting inter-annual variation in total allowable catch strategies. An application to ICES roundfish stocks

This study evaluated through simulation management strategy that stabilise catch levels by setting bounds on the inter-annual variability in Total Allowable Catches (TACs). An integrated modelling approach was used, which modelled both the ‘real’ and observed systems and the interactions between all system components. The modelling framework therefore allowed evaluation of the robustness of candidate management strategies to both the intrinsic properties of the systems, and the ability to observe, monitor, assess and control them. Strategies were evaluated in terms of level of risk (measured as the probability of spawning stock biomass falling below the biomass limit reference level for the stock) and cumulative yield. The simulation approach used provides a powerful tool for the examination of the performance of candidate management strategies. It has shown that better management is not necessarily going to be achieved by improving the assessement, since even with a perfect assessment (where the simulated working group knew stock status perfectly) stocks may crash at fishing levels that standard stochastic projections would suggest were safe. Also explicitly modelling the assessment process can result in quite different outcomes than those predicted by the simple projection traditionally used by stock assessment working groups. This is because the simple projection assumes that the status of the stock in the current year is known without error and that the target fishing mortality can be achieved without error. However, in practice the assessment is based on last years data and the effect of any management measure on SSB is only manifest, following the implementation of the quota, at the end of the following year. The choice of target and fishing mortality levels and minimum stock levels results from ICES interpretation of the precautionary approach. This lead to the definition of fishing mortality and biomass reference points that are intended to prevent over-fishing and to trigger recovery plans when a stock is overfished respectively. Although, fishing mortality and biomass reference points were originally intended to be independent, a fishing mortality level implies a corresponding biomass level. In the case of saithe a fishing mortality of 0.40 (i.e. the FPA level) would drive the stock to Blim, suggesting that the choice of biomass and target reference points are not consistent for this stock

A Novel Bocavirus Associated with Acute Gastroenteritis in Australian Children

Acute gastroenteritis (AGE) is a common illness affecting all age groups worldwide, causing an estimated three million deaths annually. Viruses such as rotavirus, adenovirus, and caliciviruses are a major cause of AGE, but in many patients a causal agent cannot be found despite extensive diagnostic testing. Proposing that novel viruses are the reason for this diagnostic gap, we used molecular screening to investigate a cluster of undiagnosed cases that were part of a larger case control study into the etiology of pediatric AGE. Degenerate oligonucleotide primed (DOP) PCR was used to non-specifically amplify viral DNA from fecal specimens. The amplified DNA was then cloned and sequenced for analysis. A novel virus was detected. Elucidation and analysis of the genome indicates it is a member of the Bocavirus genus of the Parvovirinae, 23% variant at the nucleotide level from its closest formally recognized relative, the Human Bocavirus (HBoV), and similar to the very recently proposed second species of Bocavirus (HBoV2). Fecal samples collected from case control pairs during 2001 for the AGE study were tested with a bocavirus-specific PCR, and HBoV2 (sequence confirmed) was detected in 32 of 186 cases with AGE (prevalence 17.2%) compared with only 15 controls (8.1%). In this same group of children, HBoV2 prevalence was exceeded only by rotavirus (39.2%) and astrovirus (21.5%) and was more prevalent than norovirus genogroup 2 (13.4%) and adenovirus (4.8%). In a univariate analysis of the matched pairs (McNemar's Test), the odds ratio for the association of AGE with HBoV2 infection was 2.6 (95% confidence interval 1.2–5.7); P = 0.007. During the course of this screening, a second novel bocavirus was detected which we have designated HBoV species 3 (HBoV3). The prevalence of HBoV3 was low (2.7%), and it was not associated with AGE. HBoV2 and HBoV3 are newly discovered bocaviruses, of which HBoV2 is the thirdmost-prevalent virus, after rotavirus and astrovirus, associated with pediatric AGE in this study

High levels of multidrug resistant tuberculosis in new and treatment-failure patients from the Revised National Tuberculosis Control Programme in an urban metropolis (Mumbai) in Western India

BACKGROUND: India, China and Russia account for more than 62% of multidrug resistant tuberculosis (MDRTB) globally. Within India, locations like urban metropolitan Mumbai with its burgeoning population and high incidence of TB are suspected to be a focus for MDRTB. However apart from sporadic surveys at watched sites in the country, there has been no systematic attempt by the Revised National Tuberculosis Control Programme (RNTCP) of India to determine the extent of MDRTB in Mumbai that could feed into national estimates. Drug susceptibility testing (DST) is not routinely performed as a part of programme policy and public health laboratory infrastructure, is limited and poorly equipped to cope with large scale testing. METHODS: From April 2004 to January 2007 we determined the extent of drug resistance in 724 {493 newly diagnosed, previously untreated and 231 first line treatment failures (sputum-smear positive at the fifth month after commencement of therapy)} cases of pulmonary tuberculosis drawn from the RNTCP in four suboptimally performing municipal wards of Mumbai. The observations were obtained using a modified radiorespirometric Buddemeyer assay and validated by the Swedish Institute for Infectious Disease Control, Stockholm, a supranational reference laboratory. Data was analyzed utilizing SPSS 10.0 and Epi Info 2002. RESULTS: This study undertaken for the first time in RNTCP outpatients in Mumbai reveals a high proportion of MDRTB strains in both previously untreated (24%) and treatment-failure cases (41%). Amongst new cases, resistance to 3 or 4 drug combinations (amplified drug resistance) including isoniazid (H) and rifampicin (R), was greater (20%) than resistance to H and R alone (4%) at any point in time during the study. The trend for monoresistance was similar in both groups remaining highest to H and lowest to R. External quality control revealed good agreement for H and R resistance (k = 0.77 and 0.76 respectively). CONCLUSION: Levels of MDRTB are much higher in both previously untreated and first line treatment-failure cases in the selected wards in Mumbai than those projected by national estimates. The finding of amplified drug resistance suggests the presence of a well entrenched MDRTB scenario. This study suggests that a wider set of surveillance sites are needed to obtain a more realistic view of the true MDRTB rates throughout the country. This would assist in the planning of an adequate response to the diagnosis and care of MDRTB

Pathogenesis of adolescent idiopathic scoliosis in girls - a double neuro-osseous theory involving disharmony between two nervous systems, somatic and autonomic expressed in the spine and trunk: possible dependency on sympathetic nervous system and hormones with implications for medical therapy

Anthropometric data from three groups of adolescent girls - preoperative adolescent idiopathic scoliosis (AIS), screened for scoliosis and normals were analysed by comparing skeletal data between higher and lower body mass index subsets. Unexpected findings for each of skeletal maturation, asymmetries and overgrowth are not explained by prevailing theories of AIS pathogenesis. A speculative pathogenetic theory for girls is formulated after surveying evidence including: (1) the thoracospinal concept for right thoracic AIS in girls; (2) the new neuroskeletal biology relating the sympathetic nervous system to bone formation/resorption and bone growth; (3) white adipose tissue storing triglycerides and the adiposity hormone leptin which functions as satiety hormone and sentinel of energy balance to the hypothalamus for long-term adiposity; and (4) central leptin resistance in obesity and possibly in healthy females. The new theory states that AIS in girls results from developmental disharmony expressed in spine and trunk between autonomic and somatic nervous systems. The autonomic component of this double neuro-osseous theory for AIS pathogenesis in girls involves selectively increased sensitivity of the hypothalamus to circulating leptin (genetically-determined up-regulation possibly involving inhibitory or sensitizing intracellular molecules, such as SOC3, PTP-1B and SH2B1 respectively), with asymmetry as an adverse response (hormesis); this asymmetry is routed bilaterally via the sympathetic nervous system to the growing axial skeleton where it may initiate the scoliosis deformity (leptin-hypothalamic-sympathetic nervous system concept = LHS concept). In some younger preoperative AIS girls, the hypothalamic up-regulation to circulating leptin also involves the somatotropic (growth hormone/IGF) axis which exaggerates the sympathetically-induced asymmetric skeletal effects and contributes to curve progression, a concept with therapeutic implications. In the somatic nervous system, dysfunction of a postural mechanism involving the CNS body schema fails to control, or may induce, the spinal deformity of AIS in girls (escalator concept). Biomechanical factors affecting ribs and/or vertebrae and spinal cord during growth may localize AIS to the thoracic spine and contribute to sagittal spinal shape alterations. The developmental disharmony in spine and trunk is compounded by any osteopenia, biomechanical spinal growth modulation, disc degeneration and platelet calmodulin dysfunction. Methods for testing the theory are outlined. Implications are discussed for neuroendocrine dysfunctions, osteopontin, sympathoactivation, medical therapy, Rett and Prader-Willi syndromes, infantile idiopathic scoliosis, and human evolution. AIS pathogenesis in girls is predicated on two putative normal mechanisms involved in trunk growth, each acquired in evolution and unique to humans

An improved method for estimating individual growth variability in fish, and the correlation between von Bertalanffy growth parameters

A new method for estimating individual variability in the von Bertalanffy growth parameters of fish species is presented. The method uses a nonlinear random effects model, which explicitly assumes that an individual's growth parameters represent samples from a multivariate population of growth parameters characteristic of a species or population. The method was applied to backcalculated length-at-age data from the tropical emperor, Lethrinus mahsena. Individual growth parameter variability estimates were compared with those derived using the current "standard" method, which characterizes the joint distribution of growth parameter estimates obtained by independently fitting a growth curve to each individual data set. Estimates of mean von Bertalanffy growth parameters from the two methods were similar. However, estimated growth parameter variances were much higher using the standard method. Using the random effects model, the estimated correlation between population mean values of L-infinity and K was -0.52 or -0.42, depending on the marginal distribution assumed for K. The latter estimate had a 95% posterior credibility interval of -0.62 to -0.17. These represent the first reliable estimate of this correlation and confirm the view that these parameters are negatively correlated in fish populations; however, the absolute correlation value is somewhat lower than has been assumed

A Bayesian hierarchical formulation of the De Lury stock assessment model for abundance estimation of Falkland Islands' squid (Loligo gahi)

In stock assessments of short-lived species, De Lury depletion models are commonly applied in which commercial catches and changing catch rates are used to estimate resource abundance. These methods are applied within fishing seasons to decide when to close the fishery and can be reliable if the data show a distinct decline in response to the catch removals. However, this is not always the case, particularly when sampling error variation masks trends in abundance. This paper presents a Bayesian hierarchical formulation of the De Lury model in which data from previous years are combined hierarchically in the same stock assessment model to improve parameter estimation for future stock assessments. The improved precision in parameter estimates is demonstrated using data for the Falkland Islands' Loligo gahi squid fishery

Comparison of Mitochondrial Mutation Spectra in Ageing Human Colonic Epithelium and Disease: Absence of Evidence for Purifying Selection in Somatic Mitochondrial DNA Point Mutations

<div><p>Human ageing has been predicted to be caused by the accumulation of molecular damage in cells and tissues. Somatic mitochondrial DNA (mtDNA) mutations have been documented in a number of ageing tissues and have been shown to be associated with cellular mitochondrial dysfunction. It is unknown whether there are selective constraints, which have been shown to occur in the germline, on the occurrence and expansion of these mtDNA mutations within individual somatic cells. Here we compared the pattern and spectrum of mutations observed in ageing human colon to those observed in the general population (germline variants) and those associated with primary mtDNA disease. The pathogenicity of the protein encoding mutations was predicted using a computational programme, MutPred, and the scores obtained for the three groups compared. We show that the mutations associated with ageing are randomly distributed throughout the genome, are more frequently non-synonymous or frameshift mutations than the general population, and are significantly more pathogenic than population variants. Mutations associated with primary mtDNA disease were significantly more pathogenic than ageing or population mutations. These data provide little evidence for any selective constraints on the occurrence and expansion of mtDNA mutations in somatic cells of the human colon during human ageing in contrast to germline mutations seen in the general population.</p> </div

Gene location and types of mutations observed in ageing, population, and disease.

<p>A: Gene location of mutations. Data are represented as the percentage of the total coding region mutations. Contingency analysis with Bonferroni correction for multiple testing was carried out on the frequencies of the changes in each gene type (ageing n = 117, population n = 182, disease n = 176). Thresholds for statistical significance are; ***<0.0003, ** 0.003, * = 0.017. B: Types of changes observed in ageing, population and disease. Data are represented as the percentage of the total coding region mutations. Contingency analysis with Bonferroni correction for multiple testing was carried out on the frequencies of the changes in each mutational category. Thresholds for statistical significance are; ***<0.0003, ** 0.003, * = 0.017.</p