Simulation-based estimation of stochastic process parameters in tumor growth

Models are generally developed at the micro level. Data are generally gathered at the macro level. Obtaining the macromodel which is the natural consequence of the underlying micro model is generally not feasible. SIMEST gives a means whereby the micromodel is used to generate, for a given assumed set of parameters, simulated sets of macro data. These data are compared with the actual clinical macro data. The parameters are then adjusted to obtain concordance with the clinical data. In this manner, simulation gives us a means of parameter estimation without the necessity of generating the macro model.     

Growth parameters and total mortality in Oreochromis niloticus (Linnaeus) from Nyanza Gulf,Lake Victoria

Length-frequency data collected from fish landings in the Kenya waters of Lake Victoria were used to estimate the growth parameters, total mortality rate and growth performance index in Oreochromis niloticus. The asymptotic length, (L _∞) and the ratio of the total mortality rate (Z) to the growth constant (K), were estimated to be 64.6 cm and 3.219 respectively. K was 0.254 y^-1, Z was 0.818 y^-1 and the growth performance index θ′ = Log₁₀ K + 2 log₁₀ L∞ = 3.025, which is rather high as compared to other tilapia populations in natural waters.     

Estimating reaction norms for predictive population parameters,age specific mortality,and mean longevity in temperature‐dependent cohorts of Culex quinquefasciatus Say (Diptera: Culicidae)

Culex quinquefasciatus plays a major role in the transmission of important parasites and viruses throughout the world. Because temperature is an important limiting factor on growth and longevity of all mosquito species, estimating the reaction norms provides very important basic information for understanding both plasticity and individual variations of the population. In the present study, Cx. quinquefasciatus were maintained at five different constant temperatures (15°, 20°, 23°, 27°, and 30°C) for two subsequent generations. Reproductive population parameters in blood‐fed mated females and longevities of virgin and blood‐fed mated adults reared at different temperatures were compared for the two generations. Longevity increased as temperature decreased within a range of 15° to 30°C for the unmated adults, and 15° to 27°C for the mated and blood‐fed adults. Generation times were as long as 124.07 and 106.76 days for two subsequent generations reared at 15°C, and the highest intrinsic rate of increase (r_m) values were estimated at 0.22 and 0.18, respectively, from the cohorts reared at 27°C. For survival rates, reproductive rates (R₀), and r_m values, 30°C was found to be a critical temperature for this species. These cohorts produced the smallest amount of eggs (R₀= 5.06), r_m values decreasing across generations (from 0.11 to 0.06), and the survival rates from egg to adult were found to be insufficient (16.1 and 10.8%). Additionally, the rate of exponential increase with age and age specific mortalities (b) were calculated for the virgin cohorts. Age specific mortality rates increased as temperature decreased. The increase in mortality rates started to accelerate at 27°C and was more pronounced at 30°C, for both females and males. We estimated the coefficients of variation for the b values in which females have smaller coefficients than those of the males at all temperatures.     

The estimation of natural mortality in Irish Sea plaice, Pleuronectes platessa L., using tagging methods

This paper addresses the question as to whether natural mortality ( M ) can be estimated reliably in a heavily exploited fish population. Several methods, including a new opitimization technique based on Pope's cohort model, were used to estimate M from a large series of tagging experiments carried out on the Irish Sea plaice off North Wales and Ireland during the early 1960s, and off North Wales during 1979 and 1980. The assumptions underlying the new method were: (i) that the product of initial survival after tagging and the reporting rate of recaptures ( SB ) was constant for all experiments, and (ii) that the number of recoveries were log-normally distributed. Simulations showed that the estimator was robust to errors in input data. The SB values were low (0.37) but were more precise than the estimates of natural mortality for both sexes. The annual M values were 0.17 and 0.11 with standard errors 0.06 and 0.08 for males and females, respectively. The estimate of M for mature males was low, indicating a low M for older fish. The less precise estimate of M for females because of the inadequate dataset, and the higher M values obtained by applying traditional methods to the same dataset, indicated that a value of 0.2 is more appropriate for both sexes. Suggestions are made for designing and analysing tagging experiments to estimate M .     

The effects of temperature and size on growth and mortality of cod larvae

The optimal temperatures for growth of four groups of hatchery-reared cod larvae (geometric mean weight: 73, 191, 249 and 251 μg), reared on rotifers at four or five constant temperatures between 4 and 16° C for 14, 12, 9 and 16 days were 9.7, 12.3, 12.7 and 13.4° C, respectively. The maximum growth rate also increased with size and was 6.5, 9.6, 11.7 and 11.3% day⁻¹ for the respective size groups. The optimal temperature for survival was 8.5–8.8° C for all size groups. The results indicate an opposite relationship between (1) size and optimal temperature for growth and (2) size and maximum growth rate of cod larvae, to that observed for juvenile and immature cod.     

Calculating growth parameters of Genidens barbus (Siluriformes, Ariidae) using length composition and age data

The marine catfish Genidens barbus was once one of the most important estuarine fishery resources in the Patos Lagoon (southern Brazil), which had the largest population known for the species. However, clear signs of overfishing have been observed since the 1980s. Growth parameters for this population were estimated by combining length frequency data for juveniles and selected published data on annuli reading from adult otoliths. This methodology yielded a more realistic set of parameters using both the specialized and generalized von Bertalanffy growth model. The species growth can be described as: L_t = 118.6[1 − e^{−0.043(t+1.505)}] or L_t = 104.6[1 −e^{−0.137D(t+4.013)}]^1/D with the surface factor D = 0.542. The growth performance index ϕ′ was estimated as 2.78 for the special (classical) model. Stock rebuilding is expected to be slow, as the species is slow‐growing, has a low natural mortality rate, and mouthbreeds a small amount of large eggs.     

Telomere length in white blood cells is not associated with morbidity or mortality in the oldest old: a population-based study

Cross-sectional studies have repeatedly suggested peripheral blood monocyte telomere length as a biomarker of aging. To test this suggestion in a large population-based follow-up study of the oldest old, we measured telomere length at baseline in 598 participants of the Leiden 85-plus Study (mean age at baseline 89.8 years). We also obtained second telomere measurements from 81 participants after an average time span of between 3.9 and 12.9 years. Telomere length at baseline was not predictive for mortality (P > 0.40 for all-cause, cardiovascular causes, cancer or infectious diseases, Cox regression for gender-adjusted tertiles of telomere length) or for the incidence of dementia (P = 0.78). Longitudinally, telomere length was highly unstable in a large fraction of participants. We conclude that blood monocyte telomere length is not a predictive indicator for age-related morbidity and mortality at ages over 85 years, possibly because of a high degree of telomere length instability in this group.     

Increased effect of the ApoE gene on survival at advanced age in healthy and long‐lived Danes: two nationwide cohort studies

Studies of Nordic twins suggest an increased genetic influence on mortality with age. Contrary to this, the heterogeneity hypothesis predicts that the mortality of individuals carrying a ‘frail’ or ‘risky’ genotype in a population will approach that of noncarriers with age because of selection pressure. The ApoE ε4 allele is associated with an increased mortality risk, and its effect has been suggested to decrease with age. Here, we investigated the effect of ApoE ε4 allele on survival in a sample of the healthiest and long‐lived Danes. The study population comprised Danes born in 1905 and a replicate sample of the 1895 cohort. For the 1905 cohort, a total of 350 carriers and 1256 noncarriers of the ApoE ε4 allele were followed from 1998 until death or end of follow‐up. Cox regression models were used for the analysis. Of the 1606 persons with known ApoE ε4 status in 1998, 1546 had died at the end of the 10‐year follow‐up. Carriers of the ApoE ε4 allele had an increased mortality compared to noncarriers, and the influence of ApoE status on mortality increased in the age interval 92–103. For the covariates sex and independency status, the difference in relative risk of death between groups decreased with advancing age. Our findings of increasing influence of ApoE ε4 allele on mortality with age do not support previous findings of decreased influence ApoE ε4 allele on mortality with age, and alternative models such as the multifactorial threshold models should be considered for understanding the genetic effects on mortality at advanced age.     

Gene expression profiles associated with aging and mortality in humans

We investigated the hypothesis that gene expression profiles in cultured cell lines from adults, aged 57–97 years, contain information about the biological age and potential longevity of the donors. We studied 104 unrelated grandparents from 31 Utah CEU (Centre d'Etude du Polymorphisme Humain – Utah) families, for whom lymphoblastoid cell lines were established in the 1980s. Combining publicly available gene expression data from these cell lines, and survival data from the Utah Population Database, we tested the relationship between expression of 2151 always-expressed genes, age, and survival of the donors. Approximately 16% of 2151 expression levels were associated with donor age: 10% decreased in expression with age, and 6% increased with age. Cell division cycle 42 (CDC42) and CORO1A exhibited strong associations both with age at draw and survival after draw (multiple comparisons-adjusted Monte Carlo P -value < 0.05). In general, gene expressions that increased with age were associated with increased mortality. Gene expressions that decreased with age were generally associated with reduced mortality. A multivariate estimate of biological age modeled from expression data was dominated by CDC42 expression, and was a significant predictor of survival after blood draw. A multivariate model of survival as a function of gene expression was dominated by CORO1A expression. This model accounted for approximately 23% of the variation in survival among the CEU grandparents. Some expression levels were negligibly associated with age in this cross-sectional dataset, but strongly associated with inter-individual differences in survival. These observations may lead to new insights regarding the genetic contribution to exceptional longevity.     

Bias in calculating growth rates in cod (Gadus morhua L.) due to size selective growth and mortality

Size selective growth and size selective mortality strongly biased the calculation of specific growth rates among juvenile cod in a feeding experiment.     

Estimating equations for parameters in stochastic growth models from tag-recapture data

James (1991, Biometrics 47, 1519-1530) constructed unbiased estimating functions for estimating the two parameters in the von Bertalanffy growth curve from tag-recapture data. This paper provides unbiased estimating functions for a class of growth models that incorporate stochastic components and explanatory variables. A simulation study using seasonal growth models indicates that the proposed method works well while the least-squares methods that are commonly used in the literature may produce substantially biased estimates. The proposed model and method are also applied to real data from tagged rock lobsters to assess the possible seasonal effect on growth.     

Extreme longevity in freshwater mussels revisited: sources of bias in age estimates derived from mark–recapture experiments

1. There may be bias associated with mark–recapture experiments used to estimate age and growth of freshwater mussels. Using subsets of a mark–recapture dataset for Quadrula pustulosa, I examined how age and growth parameter estimates are affected by (i) the range and skew of the data and (ii) growth reduction due to handling. I compared predictions from von Bertalanffy growth models based on mark–recapture data with direct observation of mussel age and growth inferred from validated shell rings. 2. Growth models based on a dataset that included observations from a wide range of length classes (spanning ≥ the upper 50% of the population length range) produced only slightly biased age estimates for small and medium‐sized individuals (overestimated by 1–2 years relative to estimates from validated shell rings) but estimates became increasingly biased for larger individuals. Growth models using data that included only observations of larger animals (< the upper 50% of length range) overestimated age for all length classes, and estimated maximum age was two to six times greater than the maximum age observed in the population (47 years). Similarly, growth models using a left‐skewed dataset overestimated age. 3. Reductions of growth due to repeated handling also resulted in overestimates of age. The estimated age of mussels that were handled in two consecutive years was as much as twice that of mussels that were handled only once over the same period. Assuming a constant reduction in the annual rate of growth, handling an individual for five consecutive years could result in an estimated age that is five times too high. 4. These findings show that mark–recapture methods have serious limitations for estimating mussel age and growth. A previous paper (Freshwater Biology, 46, 2001, 1349) presented longevity estimates for three mussel species that were an order of magnitude higher than estimates inferred from shell rings. Because those estimates of extreme longevity were based on mark–recapture methods and subject to multiple, additive sources of bias, they cannot be considered accurate representations of life span and cannot be used to conclude that traditional methods of bivalve ageing by interpretation of shell rings are flawed.     

The estimation of parameters from population data on the general stochastic epidemic

This paper provides a method of using maximum likelihood to estimate the two unknown parameters, the contact rate and the removal rate, in the general stochastic epidemic, using only the observed interremoval times and the total number of cases occurring. A goodness-of-fit test is discussed, and the methods described are illustrated by means of data on an actual smallpox epidemic in a restricted community in southeastern Nigeria.     

The importance of incorporating age and sex when backcalculating length in bullhead Cottus gobio

The present study backcalculated body length for a data set of a bullhead Cottus gobio population located at different sampling sites in a river network. Model comparison between various growth models, which included successively new parameters, showed the effect and importance of taking sex, age and the location in the river network into account. The data sets obtained by backcalculation were fitted by the von Bertalanffy growth function, which revealed the effect of the backcalculation formula on the estimation of the von Bertalanffy growth parameters. Fitting results and parameter estimates showed again the importance of incorporating age and sex when backcalculating body length in the C. gobio population studied.     

Age estimation,growth rate and size at sexual maturity of tigerfish Hydrocynus vittatus from the Okavango Delta,Botswana

The aims of this study were to determine relative age, growth rate and size at maturity of tigerfish in the Okavango Delta as a basis for the development of a fisheries management plan. A total of 206 tigerfish Hydrocynus vittatus, collected by angling in August 2005,2006 and 2007, was assessed for sexual maturity and relative ages were estimated from 135 of these, using scales and whole and sectioned otoliths. Sectioned otoliths were the most appropriate method for ageing H. vittatus of up to 20 years old. Males were present in all relative age classes, proving that they do not disappear from the population at a young age, as previously thought. Males matured at 451 mm TL and females at 522 mm TL, corresponding to an approximate relative age of four years for both sexes. Males lived for up to 20 years, females for up to 16 years.     

Restriction fragment length polymorphisms at the growth hormone gene in pigs

Pigs from four Danish and two Swedish populations were examined for restriction fragment length polymorphism (RFLP) at the growth hormone (GH) gene. Polymorphism was detected with the restriction enzymes DraI and TaqI. A comparison of the Danish populations showed significant differences among their allelic frequencies.     

Avian growth and development rates and age-specific mortality: the roles of nest predation and adult mortality

Previous studies have shown that avian growth and development covary with juvenile mortality. Juveniles of birds under strong nest predation pressure grow rapidly, have short incubation and nestling periods, and leave the nest at low body mass. Life-history theory predicts that parental investment increases with adult mortality rate. Thus, developmental traits that depend on the parental effort exerted (pre- and postnatal growth rate) should scale positively with adult mortality, in contrast to those that do not have a direct relationship with parental investment (timing of developmental events, e.g. nest leaving). I tested this prediction on a sample of 84 North American songbirds. Nestling growth rate scaled positively and incubation period duration negatively with annual adult mortality rates even when controlled for nest predation and other covariates, including phylogeny. On the contrary, neither the duration of the nestling period nor body mass at fledging showed any relationship. Proximate mechanisms generating the relationship of pre- and postnatal growth rates to adult mortality may include increased feeding, nest attentiveness during incubation and/or allocation of hormones, and deserve further attention.