Age,period, and cohort effects on maternal mortality: A linear logit model

Abstract

Cohort approach is used to disentangle age, period, and cohort effects on maternal mortality in New York State. By comparing various age * period * cohort linear logit models on the logits of maternal mortality rates, we conclude that period and age effects are the dominant influences on maternal mortality, and cohort effect does not contribute as much as we expect after adjustment for age and period. The implications are that, as a set, changes in those temporal variables which cut across cohorts appear to be more important than changes in those variables which distinguish them.     

A hazard logit model analysis of covariates of childhood mortality in Matlab, Bangladesh.

In a prospective study in Matlab, a rural area in Bangladesh, the relationship between a variety of covariates and childhood mortality was examined. Economic status of household, education of mother, sex of the children, health intervention programmes, age of mother, and live birth order of the children were identified as having a statistically significant impact on child survival when the effect of age was controlled. The effects of sex of the children, health programmes, age of mother, and birth order were found to be dependent on the age of the children, but the effect of mother's education was dependent on sex of the children.     

A nonproportional hazards Weibull accelerated failure time regression model

We present a study of risk factors measured in mean before age 50 and subsequent incidence of heart disease over 32 years of follow-up. The data are from the Framingham Heart Study. The standard accelerated failure time model assumes the logarithm of time until an event has a constant dispersion parameter and a location parameter that is a linear function of covariates. Parameters are estimated by maximum likelihood. We reject a standard Weibull model for these data in favor of a model with the dispersion parameter depending on the location parameter. This model suggests that the cumulative hazard ratio for two individuals shrinks towards unity over the follow-up period. Thus, not only the standard Weibull, but also the semiparametric proportional hazards (Cox) model is inadequate for this data. The model improvement appears particularly valuable when estimating the difference in predicted outcome probabilities for two individuals.     

A model for channel noise,including the effect of diffusion

A model (based on a proposal by Schick (1974), is developed for channels composed of four species; the channels allow conduction when all species are in the correct configuration. Allowance is also made for diffusion resulting from depletion of ions in the neighbourhood of the channel. The result is a series of pulses in which the current falls as ^–1/2 upon closing the channel. The resulting power spectrum is calculated according to the method given by Schick and earlier workers, and is found to be, at least qualitatively, in agreement with many of the features of noise measured for certain types of nerve membranes. The calculations are not linearized, but are carried through numerically.     

A finite-element model of blood flow in arteries including taper, branches, and obstructions

A nonlinear mathematical model of arterial blood flow, which can account for tapering, branching, and the presence of stenosed segments, is presented. With the finite-element method, the model equations are transformed into a system of algebraic equations that can be solved on a high-speed digital computer to yield values of pressure and volume rate of flow as functions of time and arterial position. A model of the human femoral artery is used to compare the effects of linear and nonlinear modeling. During periods of rapid alternations in pressure or flow, the nonlinear model shows significantly different results than the linear model. The effect of a stenosis on pressure and flow waveforms is also simulated, and the results indicate that these waveforms are significantly altered by moderate and severe stenoses.     

A yeast model for polyalanine-expansion aggregation and toxicity

Nine human disorders result from the toxic accumulation and aggregation of proteins with expansions in their endogenous polyalanine (polyA) tracts. Given the prevalence of polyA tracts in eukaryotic proteomes, we wanted to understand the generality of polyA-expansion cytotoxicity by using yeast as a model organism. In our initial case, we expanded the polyA tract within the native yeast poly(Adenine)-binding protein Pab1 from 8A to 13A, 15A, 17A, and 20A. These expansions resulted in increasing formation of Pab1 inclusions, insolubility, and cytotoxicity that correlated with the length of the polyA expansion. Pab1 binds mRNA as part of its normal function, and disrupting RNA binding or altering cytoplasmic mRNA levels suppressed the cytotoxicity of 17A-expanded Pab1, indicating a requisite role for mRNA in Pab1 polyA-expansion toxicity. Surprisingly, neither manipulation suppressed the cytotoxicity of 20A-expanded Pab1. Thus longer expansions may have a different mechanism for toxicity. We think that this difference underscores the potential need to examine the cytotoxic mechanisms of both long and short expansions in models of expansion disorders.     

A model for optimal offspring size in fish, including live-bearing and parental effects

Since Smith and Fretwell's seminal article in 1974 on the optimal offspring size, most theory has assumed a trade-off between offspring number and offspring fitness, where larger offspring have better survival or fitness, but with diminishing returns. In this article, we use two ubiquitous biological mechanisms to derive the shape of this trade-off: the offspring's growth rate combined with its size-dependent mortality (predation). For a large parameter region, we obtain the same sigmoid relationship between offspring size and offspring survival as Smith and Fretwell, but we also identify parameter regions where the optimal offspring size is as small or as large as possible. With increasing growth rate, the optimal offspring size is smaller. We then integrate our model with strategies of parental care. Egg guarding that reduces egg mortality favors smaller or larger offspring, depending on how mortality scales with size. For live-bearers, the survival of offspring to birth is a function of maternal survival; if the mother's survival increases with her size, then the model predicts that larger mothers should produce larger offspring. When using parameters for Trinidadian guppies Poecilia reticulata, differences in both growth and size-dependent predation are required to predict observed differences in offspring size between wild populations from high- and low-predation environments.     

A dynamic model of the forearm including fatigue

A biomechanical model of the forearm, consisting of 61 muscle-tendon systems or tendons and 8 sections, is presented. The model can be used to calculate the muscle forces when resultant of the external forces and the motion is known. Calculations are based on constraints of muscle forces, joint forces, contact forces, and tendon junctions, and a load sharing principle telling which of the feasible solutions are likely and which are not. Fatigue is accounted for by updating the upper limits of the muscle forces according to the loading history. As an example, the model is used to predict the load sharing between the fingers when they are pressed against a table with a given total force.     

A simulation model of sulfur transformations in forested Spodosols

Transformations of organic and inorganic S in two forested Spodosols from the Hubbard Brook Experimental Forest, New Hampshire and the Huntington Forest in the Adirondack Mts. of New York were investigated using laboratory³⁵SO₄ ^2- incorporation experiments. Sulfur transformations were modeled as a set of three reversible, first-order reactions in which soluble SO ₄ ^2- is converted to adsorbed SO ₄ ^2- , ester sulfate and carbon-bonded S. Reaction rate contants for³⁵SO ₄ ^2- adsorption/desorption and immobilization reactions involving ester sulfate and carbon-bonded S were determined using a fifth order Runge-Kutta-Fehlberg integration routine combined with least squares fitting. Model simulations were able to account for over 93% of the variation in the distribution of³⁵S in S fractions. A hypothetical application of immobilization rate constants to field situations at the Hubbard Brook Experimental Forest suggests that large quantities of S cycle through organic forms in Northern Hardwood Forest Ecosystems.     

A general model of error-prone PCR

In this paper, we generalize a previously-described model of the error-prone polymerase chain reaction (PCR) reaction to conditions of arbitrarily variable amplification efficiency and initial population size. Generalisation of the model to these conditions improves the correspondence to observed and expected behaviours of PCR, and restricts the extent to which the model may explore sequence space for a prescribed set of parameters. Error-prone PCR in realistic reaction conditions is predicted to be less effective at generating grossly divergent sequences than the original model. The estimate of mutation rate per cycle by sampling sequences from an in vitro PCR experiment is correspondingly affected by the choice of model and parameters.     

A compact beta model of huntingtin toxicity

Huntington disease results from an expanded polyglutamine region in the N terminus of the huntingtin protein. HD pathology is characterized by neuronal degeneration and protein inclusions containing N-terminal fragments of mutant huntingtin. Structural information is minimal, though it is believed that mutant huntingtin polyglutamine adopts β structure upon conversion to a toxic form. To this end, we designed mammalian cell expression constructs encoding compact β variants of Htt exon 1 N-terminal fragment and tested their ability to aggregate and induce toxicity in cultured neuronal cells. In parallel, we performed molecular dynamics simulations, which indicate that constructs with expanded polyglutamine β-strands are stabilized by main-chain hydrogen bonding. Finally, we found a correlation between the reactivity to 3B5H10, an expanded polyglutamine antibody that recognizes a compact β rich hairpin structure, and the ability to induce cell toxicity. These data are consistent with an important role for a compact β structure in mutant huntingtin-induced cell toxicity.     

A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering

The gastrulation of Nematostella vectensis, the starlet sea anemone, is morphologically simple yet involves many conserved cell behaviors such as apical constriction, invagination, bottle cell formation, cell migration and zippering found during gastrulation in a wide range of more morphologically complex animals.In this article we study Nematostella gastrulation using a combination of morphometrics and computational modeling. Through this analysis we frame gastrulation as a non-trivial problem, in which two distinct cell domains must change shape to match each other geometrically, while maintaining the integrity of the embryo. Using a detailed cell-based model capable of representing arbitrary cell-shapes such as bottle cells, as well as filopodia, localized adhesion and constriction, we are able to simulate gastrulation and associate emergent macroscopic changes in embryo shape to individual cell behaviors.We have developed a number of testable hypotheses based on the model. First, we hypothesize that the blastomeres need to be stiffer at their apical ends, relative to the rest of the cell perimeter, in order to be able to hold their wedge shape and the dimensions of the blastula, regardless of whether the blastula is sealed or leaky. We also postulate that bottle cells are a consequence of cell strain and low cell–cell adhesion, and can be produced within an epithelium even without apical constriction. Finally, we postulate that apical constriction, filopodia and de-epithelialization are necessary and sufficient for gastrulation based on parameter variation studies.     

A chromosomal translocation causing multiple abnormalities including open eyelids at birth and glomerulonephritis

We have characterized the phenotype of a mouse with a t(2;13) reciprocal translocation induced by chlorambucil. It results in abnormal eyelid formation as well as a series of neurological, physiological, and immunological abnormalities. This mutant has been termed T(2;13)1Fla/+. T(2;13)1Fla/+ mice exhibit open eyelids at birth, a dilute coat color, hyperactivity, and occasional circling and stargazing activity. At 1-6 months, T(2;13)1Fla/+ mice show signs of immune complex-mediated glomerulonephritis and die prematurely. Additionally, double-stranded DNA autoantibodies have been found in sera of T(2;13)1Fla/+ mice. Cytogenetic analysis situated the translocation breakpoint at the proximal end of Chromosome (chr) 2 at band A2, and on Chr 13 at band A4. The mutant phenotype completely correlated with the presence of the translocation. Additional genetic studies have mapped the mutation and translocation breakpoint to Chr 13 between D13Mit16 and D13Mit64, and to Chr 2 proximal to D2Mit5. By fluorescent in situ hybridization (FISH), the position of this mutation/translocation on Chr 13 has been mapped to a region less than 1cM from D13Mit61.     

A simple model of pathogen-immune dynamics including specific and non-specific immunity

We present and analyze a model for the dynamics of the interactions between a pathogen and its host's immune response. The model consists of two differential equations, one for pathogen load, the other one for an index of specific immunity. Differently from other simple models in the literature, this model exhibits, according to the hosts' or pathogen's parameter values, or to the initial infection size, a rich repertoire of behaviours: immediate clearing of the pathogen through aspecific immune response; or acute infection followed by clearing of the pathogen through specific immune response; or uncontrolled infections; or acute infection followed by convergence to a stable state of chronic infection; or periodic solutions with intermittent acute infections. The model can also mimic some features of immune response after vaccination. This model could be a basis on which to build epidemic models including immunological features.     

Thymoquinone causes multiple effects,including cell death,on dividing plant cells

Thymoquinone (TQ) is a major constituent of Nigella sativa oil with reported anti-oxidative activity and anti-inflammatory activity in animal cells. It also inhibits proliferation and induces programmed cell death (apoptosis) in human skin cancer cells. The present study sought to detect the influence of TQ on dividing cells of three plant systems and on expression of Bcl2-associated athanogene-like (BAG-like) genes that might be involved during the process of cell death. BAG genes are known for the regulation of diverse physiological processes in animals, including apoptosis, tumorigenesis, stress responses, and cell division. Synthetic TQ at 0.1 mg/mL greatly reduced wheat seed germination rate, whereas 0.2 mg/mL completely inhibited germination. An Evans blue assay revealed moderate cell death in the meristematic zone of Glycine max roots after 1 h of TQ treatment (0.2 mg/mL), with severe cell death occurring in this zone after 2 h of treatment. Light microscopy of TQ-treated (0.2 mg/mL) onion hairy root tips for 1 h revealed anti-mitotic activity and also cell death-associated changes, including nuclear membrane disruption and nuclear fragmentation. Transmission electron microscopy of TQ-treated cells (0.2 mg/mL) for 1 h revealed shrinkage of the plasma membrane, leakage of cell lysate, degradation of cell walls, enlargement of vacuoles and condensation of nuclei. Expression of one BAG-like gene, previously associated with cell death, was induced 20 min after TQ treatment in Glycine max root tip cells. Thus, TQ has multiple effects, including cell death, on dividing plant cells and plants may serve as a useful system to further investigate the mechanisms underlying the response of eukaryotic cells to TQ.