Modeling and estimating a threshold effect: An application to improving cardiac surgery practices.

Estimating thresholds when a threshold effect exists has important applications in biomedical research. However, models/methods commonly used in the biomedical literature may lead to a biased estimate. For patients undergoing coronary artery bypass grafting (CABG), it is thought that exposure to low oxygen delivery (DO2) contributes to an increased risk of avoidable acute kidney injury. This research is motivated by estimating the threshold of nadir DO2 for CABG patients to help develop an evidence-based guideline for improving cardiac surgery practices. We review several models (sudden-jump model, broken-stick model, and the constrained broken-stick model) that can be adopted to estimate the threshold and discuss modeling assumptions, scientific plausibility, and implications in estimating the threshold. Under each model, various estimation methods are studied and compared. In particular, under a constrained broken-stick model, a modified two-step Newton-Raphson algorithm is introduced. Through comprehensive simulation studies and an application to data on CABG patients from the University of Michigan, we show that the constrained broken-stick model is flexible, more robust, and able to incorporate scientific knowledge to improve efficiency. The two-step Newton-Raphson algorithm has good computational performances relative to existing methods.

Significance of crinoid preservation: Clare Shale Formation (Upper Carboniferous), Fisherstreet Bay, Doolin, County Clare, Ireland.

Some fossils, such as crinoid stems, are not widely appreciated by collectors and researchers, yet can provide unique data regarding taphonomy and palaeoecology. A long crinoid pluricolumnal showing a distinctive pattern of preservation was collected from the Clare Shale Formation (Upper Carboniferous) at Fisherstreet Bay, Doolin, County Clare, western Ireland. The specimen is partly disarticulated and represents the mesistele to mesistele/dististele transition; attachment was by unbranched long, slender radices; pluricolumnal heteromorphic; fragments of pluricolumnal are of multiples of a unit length. This specimen, cladid? sp. indet., slumped to the seafloor after death and started to disarticulate as ligaments rotted. By reference to the broken stick model, the pattern of disarticulation suggests that the noditaxis of the heteromorphic stem was N212.

A Robust Automated Image-Based Phenotyping Method for Rapid Vegetative Screening of Wheat Germplasm for Nitrogen Use Efficiency.

Nitrogen use efficiency (NUE) in crops is generally low, with more than 60% of applied nitrogen (N) being lost to the environment, which increases production costs and affects ecosystems and human habitats. To overcome these issues, the breeding of crop varieties with improved NUE is needed, requiring efficient phenotyping methods along with molecular and genetic approaches. To develop an effective phenotypic screening method, experiments on wheat varieties under various N levels were conducted in the automated phenotyping platform at Plant Phenomics Victoria, Horsham. The results from the initial experiment showed that two relative N levels-5 mM and 20 mM, designated as low and optimum N, respectively-were ideal to screen a diverse range of wheat germplasm for NUE on the automated imaging phenotyping platform. In the second experiment, estimated plant parameters such as shoot biomass and top-view area, derived from digital images, showed high correlations with phenotypic traits such as shoot biomass and leaf area seven weeks after sowing, indicating that they could be used as surrogate measures of the latter. Plant growth analysis confirmed that the estimated plant parameters from the vegetative linear growth phase determined by the "broken-stick" model could effectively differentiate the performance of wheat varieties for NUE. Based on this study, vegetative phenotypic screens should focus on selecting wheat varieties under low N conditions, which were highly correlated with biomass and grain yield at harvest. Analysis indicated a relationship between controlled and field conditions for the same varieties, suggesting that greenhouse screens could be used to prioritise a higher value germplasm for subsequent field studies. Overall, our results showed that this phenotypic screening method is highly applicable and can be applied for the identification of N-efficient wheat germplasm at the vegetative growth phase.

Bruch's membrane opening-minimum rim width and visual field loss in glaucoma: a broken stick analysis.

AIM: To determine the Bruch's membrane opening-minimum rim width (BMO-MRW) tipping point where corresponding visual field (VF) damages become detectable. METHODS: A total of 85 normal subjects and 83 glaucoma patients (one eye per participant) were recruited for the study. All of the patients had VF examinations and spectral-domain optical coherence tomography to measure the BMO-MRW. Total deviation values for 52 VF points were allocated to the corresponding sector according to the Garway-Heath distribution map. To evaluate the relationship between VF loss and BMO-MRW measurements, a "broken-stick" statistical model was used. The tipping point where the VF values started to sharply decrease as a function of BMO-MRW measurements was estimated and the slopes above and below this tipping point were compared. RESULTS: A 25.9% global BMO-MRW loss from normative value was required for the VF loss to be detectable. Sectorally, substantial BMO-MRW thinning in inferotemporal sector (33.1%) and relatively less BMO-MRW thinning in the superotemporal sector (8.9%) were necessary for the detection of the VF loss. Beyond the tipping point, the slopes were close to zero throughout all of the sectors and the VF loss was unrelated to the BMO-MRW loss. The VF loss was related to the BMO-MRW loss below the tipping point. The difference between the two slopes was statistically significant (P≤0.002). CONCLUSION: Substantial BMO-MRW loss appears to be necessary for VF loss to be detectable in patients with open angle glaucoma with standard achromatic perimetry.

Applications of step-selection functions in ecology and conservation.

Recent progress in positioning technology facilitates the collection of massive amounts of sequential spatial data on animals. This has led to new opportunities and challenges when investigating animal movement behaviour and habitat selection. Tools like Step Selection Functions (SSFs) are relatively new powerful models for studying resource selection by animals moving through the landscape. SSFs compare environmental attributes of observed steps (the linear segment between two consecutive observations of position) with alternative random steps taken from the same starting point. SSFs have been used to study habitat selection, human-wildlife interactions, movement corridors, and dispersal behaviours in animals. SSFs also have the potential to depict resource selection at multiple spatial and temporal scales. There are several aspects of SSFs where consensus has not yet been reached such as how to analyse the data, when to consider habitat covariates along linear paths between observations rather than at their endpoints, how many random steps should be considered to measure availability, and how to account for individual variation. In this review we aim to address all these issues, as well as to highlight weak features of this modelling approach that should be developed by further research. Finally, we suggest that SSFs could be integrated with state-space models to classify behavioural states when estimating SSFs.

Diversidade de um cerrado sensu stricto com base em modelos de abundância de espécies / Diversity of a cerrado sensu stricto based on species abundance models

Este estudo teve como objetivo avaliar a diversidade de uma comunidade lenhosa de cerrado sensu stricto no sudeste de Goiás, a partir de modelos de distribuição de abundância de espécies. Foram alocadas aleatoriamente 10 parcelas de 20 x 20 m em um trecho de 4 km2 de cerrado sensu stricto preservado, onde todos os indivíduos com DB ≥ 5 cm (diâmetro a altura da base = 30 cm do nível do solo) foram amostrados e identificados. A comunidade apresentou ajuste aos modelos de vara-quebrada (χ 2 = 37,62, P = 0,99) e normal-logarítmico (χ 2 = 2,61, P = 0,63), que refletem equilíbrio ecológico. O modelo normal-logarítmico foi o de melhor ajuste, mostrando que as espécies se distribuem ao longo de mosaicos de recursos, fato corroborado pela diferenciação na distribuição das espécies a partir de uma análise de gradientes (análise de correspondência segmentada - DCA).

This study aimed to evaluate the diversity of the woody community of a cerrado sensu stricto in southeastern of Goiás State (Brazil), through species abundance models. Ten plots of 20 x 20 m were randomly allocated in an undisturbed cerrado sensu stricto area of 4 km2, and all individuals with DSH ≥ 5 cm (diameter at soil height = 30 cm aboveground) were sampled and identified. The broken-stick (χ 2 = 37.62, P = 0.99) and lognormal (χ 2 = 2.61, P = 0.63) models fits to community, reflecting an ecological equilibrium. The lognormal model was the most adequate, showing that the species are distributed along resource patches, in agreement to the pattern found in the gradient analysis (Detrended correspondence analysis - DCA)