A system of model fertility schedules with graphically intuitive parameters

I propose and examine a new family of models for age-specific fertility schedules, in which three index ages determine the schedule's shape. The new system is based on constrained quadratic splines. It has easily interpretable parameters, is flexible enough to fit a variety of "noiseless" schedules well, and is inflexible enough to avoid implausible estimates from noisy data. Across a set of over two hundred contemporary ASFR schedules, the new model fits a majority better, and in some cases much better, than the Coale-Trussell model. When fit to a recent Swedish time series, model parameters exhibit simple, regular changes over time, suggesting utility in forecasting applications. In simulated small-sample data the new model produces plausible ASFR estimates, with errors similar to Coale-Trussell.age-specific fertility, age-specific rates, Coale-Trussell, estimation, fertility, models, splines

Quadratic spline fits by nonlinear least squares

This web program fits a Quadratic Spline model, as described in Schmertmann (2003; Demographic Research Volume 9, Article 5), to any empirical fertility schedule supplied by the user. The fit minimizes the sum of squared differences between the empirical nfx values and the nfx values from the QS model schedule. Output includes parameter estimates, a graphical depiction of the fitted schedule, and several text reports. Users do not need specialized statistical software or a particular operating system to run the program; the only requirement is a web browser. Software http://www.demographic-research.org/Volumes/Vol12/5/qsfit/qsfit.htmlfertility, fertility models, quadratic splines, software

The Cryptococcus gattii species complex in koalas: host-pathogen-environment interactions and molecular epidemiology

The Cryptococcus gattii species complex comprises some of the aetiological agents of cryptococcosis, a severe fungal disease that affects a wide variety of hosts and is acquired from the environment by inhalation. Koalas (Phascolarctos cinereus) appear to be particularly susceptible to cryptococcosis. In Australia, eucalypt tree hollows are the classic ecological niche for C. gattii molecular type VGI and therefore are also a potential source of infection. Aspects of the tree hollow microenvironment that may allow for the growth and dispersal of C. gattii VGI remain poorly understood. The C. gattii species complex has been associated with outbreaks and case clusters, and animals are often considered useful sentinels for the disease in these scenarios. The prevalence of cryptococcosis in Australian wildlife remains unknown. Given the koala’s propensity towards developing cryptococcosis, and its regular contact with a common ecological niche for the C. gattii species complex (eucalypts), it is an ideal sentinel species. The host-pathogen-environment interactions of cryptococcosis caused by the C. gattii species complex, particularly progression from exposure to colonisation of the respiratory mucosa to eventual tissue invasion, remain poorly understood. This thesis uses amplicon-based next generation sequencing to characterise the fungal microbiome of Australian tree hollows, focusing on the role that the C. gattii species complex may play in this microenvironment. The prevalence of cryptococcosis in a population of free-ranging koalas is systematically characterised, while the pathogenesis, treatment and diagnosis of the disease in this host species are also explored. Finally, fine-scale molecular epidemiology tools (multi-locus sequence typing and whole genome sequencing) are used to determine sources of infection and examine disease caused by the C. gattii species complex in Australia, using primarily the koala as a model for naturally-occurring cryptococcosis

D-splines: Estimating rate schedules using high-dimensional splines with empirical demographic penalties

Background: High-dimensional parametric models with penalized likelihood functions strike a good balance between bias and variance for estimating continuous age schedules from large samples. The penalized spline (P-spline) approach is particularly useful for these purposes, but it in small samples it can often produce implausible age schedule estimates. Objective: I propose and evaluate a new type of P-spline model for estimating demographic rate schedules. These estimators, which I call D-splines, regularize and smooth high-dimensional splines by using demographic patterns rather than generic mathematical rules. Methods: I compare P-spline estimates of age-specific mortality rates to three alternative D-spline estimators, over a large number of simulated small populations with known rates. The penalties for the D-spline estimators are derived from patterns in the Human Mortality Database. Results: For mortality estimates in small populations, D-spline estimators generally have lower errors than standard P-splines. Conclusions: Using penalties based on demographic information about patterns and variability in rate schedules improves P-spline estimators for small populations. Contribution: This paper expands demographers' toolkit by developing a new category of P-spline estimators that are more reliable for estimating mortality in small populations

O-cell Testings Case Histories Demonstrate the Importance of Bored Pile (Drilled Shaft) Construction Technique

Herein we review the Osterberg Cell, or O-cell, method for performing large capacity load tests on bored piles (drilled shafts), and demonstrate how it provides a new opportunity to assess the effects of construction technique. A sampling of 8 case histories, 7 with comparative testing, illustrates the impact of poor technique and thus demonstrates the importance of good construction technique. The poor techniques include inadequate bottom cleanout, failure to use drilling fluids, poor concrete placement, failure to roughen sides, and improper drilling tools. We conclude with a brief description of a recent, world record, 133 MN (15,000 tons) O-cell load test

DEM examination of SPT correction factors

The Standard Penetration Test (SPT) is the most widely used method for dynamic testing of soils. The test is simple and robust but difficult to control and not fully standardized. As a result, experimental results typically show large variations and poor repeatability. To mitigate that correction factors such as energy normalization and rod length have been introduced in SPT practice. This study provides an examination of the two correction factors using models based on the discrete element method (DEM)

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

Cryptococcosis is a fungal infection caused by members of the Cryptococcus gattii and C. neoformans species complexes. The C. gattii species complex has a strong environmental association with eucalypt hollows (particularly Eucalyptus camaldulensis), which may present a source of infection. It remains unclear whether a specific mycobiome is required to support its environmental survival and growth. Conventional detection of environmental Cryptococcus spp. involves culture on differential media, such as Guizotia abyssinica seed agar. Next-generation sequencing (NGS)-based culture-independent identification aids in contextualising these species in the environmental mycobiome. Samples from 23 Australian tree hollows were subjected to both culture- and amplicon-based metagenomic analysis to characterize the mycobiome and assess relationships between Cryptococcus spp. and other fungal taxa. The most abundant genera detected were Coniochaeta, Aspergillus, and Penicillium, all being commonly isolated from decaying wood. There was no correlation between the presence of Cryptococcus spp. in a tree hollow and the presence of any other fungal genus. Some differences in the abundance of numerous taxa were noted in a differential heat tree comparing samples with or without Cryptococcus-NGS reads. The study expanded the known environmental niche of the C. gattii and C. neoformans species complexes in Australia with detections from a further five tree species. Discrepancies between the detection of Cryptococcus spp. using culture or NGS suggest that neither is superior per se and that, rather, these methodologies are complementary. The inherent biases of amplicon-based metagenomics require cautious interpretation of data through consideration of its biological relevance

Standard Penetration Testing in a virtual calibration chamber

The virtual calibration chamber technique, based on the discrete element method, is here applied to study the standard penetration test (SPT). A macro-element approach is used to represent a rod driven with an impact like those applied to perform SPT. The rod is driven into a chamber filled with a scaled discrete analogue of a quartz sand. The contact properties of the discrete analogue are calibrated simulating two low-pressure triaxial tests. The rod is driven changing input energy and controlling initial density and confinement stress. Energy-based blowcount normalization is shown to be effective. Results obtained are in good quantitative agreement with well-accepted experimentally-based relations between blowcount, density and overburden. It is also shown that the tip resistance measured under impact dynamic penetration conditions is close to that under constant velocity conditions, hence supporting recent proposals to relate CPT and SPT results.Peer ReviewedPostprint (author's final draft