Bayesian analysis of zero inflated spatiotemporal HIV/TB child mortality data through the INLA and SPDE approaches: Applied to data observed between 1992 and 2010 in rural North East South Africa

Longitudinal mortality data with few deaths usually have problems of zero-inflation. This paper presents and applies two Bayesian models which cater for zero-inflation, spatial and temporal random effects. To reduce the computational burden experienced when a large number of geo-locations are treated as a Gaussian field (GF) we transformed the field to a Gaussian Markov Random Fields (GMRF) by triangulation. We then modelled the spatial random effects using the Stochastic Partial Differential Equations (SPDEs). Inference was done using a computationally efficient alternative to Markov chain Monte Carlo (MCMC) called Integrated Nested Laplace Approximation (INLA) suited for GMRF. The models were applied to data from 71,057 children aged 0 to under 10 years from rural north-east South Africa living in 15,703 households over the years 1992–2010. We found protective effects on HIV/TB mortality due to greater birth weight, older age and more antenatal clinic visits during pregnancy (adjusted RR (95% CI)): 0.73(0.53;0.99), 0.18(0.14;0.22) and 0.96(0.94;0.97) respectively. Therefore childhood HIV/TB mortality could be reduced if mothers are better catered for during pregnancy as this can reduce mother-to-child transmissions and contribute to improved birth weights. The INLA and SPDE approaches are computationally good alternatives in modelling large multilevel spatiotemporal GMRF data structures.     

Planktonic stages of the teleost family carapidae in eastern New Zealand waters

The occurrence of planktonic carapid eggs in Otago waters, of young stages of Echiodon rendahli off Castlepoint, and the possible presence of unrecorded members of the family Carapidae in New Zealand waters is discussed. Young E. rendahli possess a long spine which originates dorsally to a distinctive suspended gut.     

Predicting survival of western rock lobsters Panulirus cygnus using discriminant analysis of haemolymph parameters taken immediately following simulated handling treatments

Instances of morbidity amongst rock lobsters (Panulirus cygnus) arriving at factories in Western Australia (WA) have been attributed to stress during post‐harvest handling. This study used discriminant analysis to determine whether physiological correlates of stress following a period of simulated post‐harvest handling had any validity as predictors of future rejection or morbidity of western rock lobsters. Groups of 230 western rock lobsters were stored for 6 h in five environments (submerged/flowing sea water, submerged/recirculating sea water, humid air, flowing seawater spray, and recirculated seawater spray). The experiment was conducted in late spring (ambient sea water 22°C), and repeated again in early autumn (ambient sea water 26°C). After 6 h treatment, each lobster was graded for acceptability for live export, numbered, and its haemolymph was sampled. The samples were analysed for a number of physiological and health status parameters. The lobsters were then stored for a week in tanks in the live lobster factory to record mortality. The mortality of lobsters in the factory was associated with earlier deviations in haemolymph parameters as they emerged from the storage treatments. Discriminant analysis (DA) of the haemolymph assays enabled the fate of 80–90% of the lobsters to be correctly categorised within each experiment. However, functions derived from one experiment were less accurate at predicting mortality when applied to the other experiments. One of the reasons for this was the higher mortality and the more severe patho‐physiological changes observed in lobsters stored in humid air or sprays at the higher temperature. The analysis identified lactate accumulation during emersion and associated physiological and haemocyte‐related effects as a major correlate of mortality. Reducing these deviations, for example by submerged transport, is expected to ensure high levels of survival. None of the indicators tested predicted mortality with total accuracy. The simplest and most accurate means of comparing emersed treatments was to count the mortality afterwards.     

Culture environment and hatchery of origin influence growth,condition and feeding organ morphology in the Pacific oyster Crassostrea gigas in South Africa

South Africa lacks a commercial oyster hatchery. To inform the sourcing of seed for future hatchery establishments, we compared half-sib Pacific oyster Crassostrea gigas cohorts from hatcheries in Namibia and Chile. We measured oyster growth, mortality, condition and feeding organ morphology in Algoa Bay (AB, Eastern Cape) and Saldanha Bay (SB, Western Cape), South Africa, from July 2011 to June 2012. Within SB, 14.3% of mean daily sea temperatures exceeded this species’ thermal optimum of 19 °C, compared to 50.5% in AB. Food abundance (mean daily chlorophyll a concentration) in SB (7.8 mg m^–3) was double that in AB (3.9 mg m^–3) where, presumably to increase particle clearance rates in a relatively phytoplankton-poor environment, oysters had larger gill:palp surface area ratios. Plankton fatty acid profiles (indicators of food quality) differed between locations. In AB, instantaneous growth rates differed between cohorts, and trends varied seasonally. Within both locations, condition index was usually higher in Chilean oysters, whereas shell density was higher in Namibian oysters. In AB only, Chilean seed suffered substantially higher summer mortalities than Namibian seed, suggesting that the latter are more suited to temperatures in AB. AB should also be assessed for culture of the indigenous oyster species that occur there.     

Self-thinning Rules at Chinese Fir (Cunninghamia lanceolata) Plantations—Based on a Permanent Density Trial in Southern China

Data selection and methods for fitting coefficients were considered to test the self-thinning law. The Chinese fir (Cunninghamia lanceolata) in even-aged pure stands with 26 years of observation data were applied to fit Reineke’s (1933) empirically derived stand density rule (N $propto$ d¯ ^-1.605, N = numbers of stems, d¯ = mean diameter), Yoda’s (1963) self-thinning law based on Euclidian geometry (v¯ $propto$ N ^-3/2, v¯ = tree volume), and West, Brown and Enquist’s (1997, 1999) (WBE) fractal geometry (w¯ $propto$ d¯ ^-8/3). OLS, RMA and SFF algorithms provided observed self-thinning exponents with the seven mortality rate intervals (2%-80%, 5%-80%, 10%-80%, 15%-80%, 20%-80%, 25%-80% and 30%-80%), which were tested against the exponents, and expected by the rules considered. Hope for a consistent allometry law that ignores species-specific morphologic allometric and scale differences faded. Exponents α of N $propto$ d¯^α, were significantly different from -1.605 and -2, not expected by Euclidian fractal geometry; exponents β of w¯ $propto$ N^β varied around Yoda’s self-thinning slope -3/2, but was significantly different from -4/3; exponent γ of w¯ $propto$ d¯^γ tended to neither 8/3 nor 3.     

Small macro‐benthic invertebrates influence the survival,growth and behaviour of juvenile green sea urchins Strongylocentrotus droebachiensis in the laboratory

Recent settlers of many marine benthic invertebrates are cryptic, which exposes them to a suite of animals that differs from those they may experience as adults, potentially resulting in interactions causing mortality and/or reducing growth. Previous field experiments have indicated that such is the case with small juvenile green sea urchins Strongylocentrotus droebachiensis but which taxa are responsible for the mortality and reduced growth was not determined. A laboratory study was conducted to examine the effects of small macro‐benthic invertebrates, specifically chitons, scaleworms and larger juvenile conspecifics, as well as the full suite of cobble‐dwelling organisms, on the mortality, growth and behaviour of small (<3 mm) juvenile sea urchins. The likelihood of survival of small juvenile sea urchins was lower in the presence of larger juvenile sea urchins or with the full suite of cobble‐dwelling organisms than in the absence of animals. The small juvenile sea urchins survived and grew the best when they were with chitons and scaleworms. The behaviour of small sea urchins with the full suite of cobble‐dwelling organisms was more cryptic than the behaviour of urchins with scaleworms. This study indicates that interactions with the suite of small organisms living amongst cobbles can affect survival, growth and behaviour of small juvenile sea urchins, and that larger juvenile sea urchins can be a source of mortality for smaller conspecifics.     

Some effects of eutrophication and the removal of aquatic plants by grass carp (Ctenopharyngodon idella) on rainbow trout (Salmo gairdnerii) in Lake Parkinson,New Zealand

Temporary removal of aquatic plants in Lake Parkinson, a small, eutrophic dune lake, resulted in a number of changes to the population of stocked rainbow trout (Salmo gairdnerii). During each summer the lake stratified and low oxygen levels limited the distribution of trout to shallow (0–4 m) surface waters. In the first summer following weed removal the numbers of black shags (Phallacrocorax carbo) counted at the lake increased, and their predation resulted in a decline in trout density. However, the growth rate and condition of the trout population then exceeded that of trout present before weed removal. During the second summer after weed removal a cladoceran bloom was followed by low phytoplankton levels and high ammonia concentrations. A prolonged calm compounded this situation with the result that oxygen levels in bottom and surface waters dropped below 2 ppm. These low oxygen levels eliminated the trout population, but other fish species present survived. Elimination of aquatic plants affected the population dynamics of other fish species in the lake with potential implications for the trout. The experiment demonstrated the importance of weed beds in maintaining a stable fish community in lakes such as Lake Parkinson.     

中国大陆地震灾害分区人员死亡评估模型研究

针对现阶段地震人员死亡评估模型在评估特定区域地震时评估结果误差较大的问题,结合中国地震灾害特点、人口分布情况等,将中国大陆划分为西北、西南和大陆东部三个地区,并对各区域按照人口密度进行分级。采用多元非线性回归方法,选取震中烈度、震区面积、抗震设防烈度参数建立分区域的地震灾害人员死亡评估模型。研究结果表明,该模型在西北、西南地区的验证结果较好,适用于中国地震灾害情况,可以用于震后快速盲评估,在一定程度上能够避免评估不同震级、相同震中烈度和人口密度的地震时,出现相同结果的情况;虽然该模型在震例较少的大陆东部地区以及城市直下型地震中评估结果需要进一步改进,但为解决特定区域地震死亡评估中误差较大问题提供了思路,能够为震后应急指挥和救援提供数据参考。