Bayesian outcome selection modeling.

In psychiatric and social epidemiology studies, it is common to measure multiple different outcomes using a comprehensive battery of tests thought to be related to an underlying construct of interest. In the research that motivates our work, researchers wanted to assess the impact of in utero alcohol exposure on child cognition and neuropsychological development, which are evaluated using a range of different psychometric tests. Statistical analysis of the resulting multiple outcomes data can be challenging, because the outcomes measured on the same individual are not independent.

Geometric properties of the complete-graph Ising model in the loop representation.

The exact solution of the Ising model on the complete graph (CG) provides an important, though mean-field, insight for the theory of continuous phase transitions. Besides the original spin, the Ising model can be formulated in the Fortuin-Kasteleyn random cluster and the loop representation, in which many geometric quantities have no correspondence in the spin representations. Using a lifted-worm irreversible algorithm, we study the CG-Ising model in the loop representation and, based on theoretical and numerical analyses, obtain a number of exact results including volume fractal dimensions and scaling forms.

ModelRevelator: Fast phylogenetic model estimation via deep learning.

Selecting the best model of sequence evolution for a multiple-sequence-alignment (MSA) constitutes the first step of phylogenetic tree reconstruction. Common approaches for inferring nucleotide models typically apply maximum likelihood (ML) methods, with discrimination between models determined by one of several information criteria. This requires tree reconstruction and optimisation which can be computationally expensive.

The power of effective study design in animal experimentation: Exploring the statistical and ethical implications of asking multiple questions of a data set.

One of the chief advantages of using highly standardised biological models including model organisms is that multiple variables can be precisely controlled so that the variable of interest is more easily studied. However, such an approach often obscures effects in sub-populations resulting from natural population heterogeneity. Efforts to expand our fundamental understanding of multiple sub-populations are in progress.

Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth.

Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat.

The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.

The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA.

Geometric scaling behaviors of the Fortuin-Kasteleyn Ising model in high dimensions.

Recently, we argued [Chin. Phys. Lett.

Homogenisation for the monodomain model in the presence of microscopic fibrotic structures.

Computational models in cardiac electrophysiology are notorious for long runtimes, restricting the numbers of nodes and mesh elements in the numerical discretisations used for their solution. This makes it particularly challenging to incorporate structural heterogeneities on small spatial scales, preventing a full understanding of the critical arrhythmogenic effects of conditions such as cardiac fibrosis. In this work, we explore the technique of homogenisation by volume averaging for the inclusion of non-conductive micro-structures into larger-scale cardiac meshes with minor computational overhead.

Gender-specific effects of COVID-19 lockdowns on scientific publishing productivity: Impact and resilience.

Rationale: The SARS-CoV2 pandemic led to drastic social restrictions globally. Early data suggest that women in science have been more adversely affected by these lockdowns than men, with relatively fewer scientific articles authored by women. However, these observations test broad populations with many potential causes of disparity.

Admixture has obscured signals of historical hard sweeps in humans.

The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species.

Classifying ball trajectories in invasion sports using dynamic time warping: A basketball case study.

Comparison and classification of ball trajectories can provide insight to support coaches and players in analysing their plays or opposition plays. This is challenging due to the innate variability and uncertainty of ball trajectories in space and time. We propose a framework based on Dynamic Time Warping (DTW) to cluster, compare and characterise trajectories in relation to play outcomes.

Analysis of sloppiness in model simulations: Unveiling parameter uncertainty when mathematical models are fitted to data.

This work introduces a comprehensive approach to assess the sensitivity of model outputs to changes in parameter values, constrained by the combination of prior beliefs and data. This approach identifies stiff parameter combinations strongly affecting the quality of the model-data fit while simultaneously revealing which of these key parameter combinations are informed primarily by the data or are also substantively influenced by the priors. We focus on the very common context in complex systems where the amount and quality of data are low compared to the number of model parameters to be collectively estimated, and showcase the benefits of this technique for applications in biochemistry, ecology, and cardiac electrophysiology.

Physiological linkage of thyroid and pituitary sensitivities.

Objectives: The sensitivities of the pituitary to thyroxine feedback, and the thyroid to thyrotropin stimulation determine the free thyroxine /thyrotropin feedback loop and can be described mathematically by two curves. It is not well understood how the two curves combine in a healthy population with normal thyroid function to express the individual balance points that are observed. This study was directed at this issue testing the possibilities of random combination and directed linkage between the two curves.

Adaptive monitoring of coral health at Scott Reef where data exhibit nonlinear and disturbed trends over time.

Time series data are often observed in ecological monitoring. Frequently, such data exhibit nonlinear trends over time potentially due to complex relationships between observed and auxiliary variables, and there may also be sudden declines over time due to major disturbances. This poses substantial challenges for modeling such data and also for adaptive monitoring.

Semiparametric Estimation of the Distribution of Episodically Consumed Foods Measured With Error.

Dietary data collected from 24-hour dietary recalls are observed with significant measurement errors. In the nonparametric curve estimation literature, much of the effort has been devoted to designing methods that are consistent under contamination by noise, and which have been traditionally applied for analyzing those data. However, some foods such as alcohol or fruits are consumed only episodically, and may not be consumed during the day when the 24-hour recall is administered.

Healthcare services for people with acquired disability in South-East Queensland, Australia: Assessing potential proximity and its association with service obstacles.

This study described access potential in South-East Queensland, to healthcare services commonly used by people with acquired disability; and investigated the association between service proximity and perceived service obstacles. First, we described accessibility by conducting a spatial analysis to create maps of potential accessibility to health services in South-East Queensland. Queensland statistical area level 2 (SA2) locations were combined with the residential locations of participants from a longitudinal cohort study involving people with ABI and SCI.

Graph-based homogenisation for modelling cardiac fibrosis.

Fibrosis, the excess of extracellular matrix, can affect, and even block, propagation of action potential in cardiac tissue. This can result in deleterious effects on heart function, but the nature and severity of these effects depend strongly on the localisation of fibrosis and its by-products in cardiac tissue, such as collagen scar formation. Computer simulation is an important means of understanding the complex effects of fibrosis on activation patterns in the heart, but concerns of computational cost place restrictions on the spatial resolution of these simulations.

A subfunctionalisation model of gene family evolution predicts balanced tree shapes.

We consider a subfunctionalisation model of gene family evolution. A family of n genes that perform z functions is represented by an n×z binary matrix Y where a 1 in the ijth position indicates that gene i can perform function j. Y evolves according to a continuous time Markov chain (CTMC) that represents the processes of gene duplication, coding region loss and regulatory region loss with the restriction that each function is protected by selection, meaning that each column in the matrix must contain at least one 1.

Promoting and countering misinformation during Australia's 2019-2020 bushfires: a case study of polarisation.

Unlabelled: During Australia's unprecedented bushfires in 2019-2020, misinformation blaming arson surfaced on Twitter using #ArsonEmergency. The extent to which bots and trolls were responsible for disseminating and amplifying this misinformation has received media scrutiny and academic research. Here, we study Twitter communities spreading this misinformation during the newsworthy event, and investigate the role of online communities using a natural experiment approach-before and after reporting of bots promoting the hashtag was broadcast by the mainstream media.

Identifying cell-to-cell variability in internalization using flow cytometry.

Biological heterogeneity is a primary contributor to the variation observed in experiments that probe dynamical processes, such as the internalization of material by cells. Given that internalization is a critical process by which many therapeutics and viruses reach their intracellular site of action, quantifying cell-to-cell variability in internalization is of high biological interest. Yet, it is common for studies of internalization to neglect cell-to-cell variability.

Population Genetics and Signatures of Selection in Early Neolithic European Farmers.

Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation.