Identifying prognostic structural features in tissue sections of colon cancer patients using point pattern analysis

Diagnosis and prognosis of cancer is informed by the architecture inherent in cancer patient tissue sections. This architecture is typically identified by pathologists, yet advances in computational image analysis facilitate quantitative assessment of this structure. In this article we develop a spatial point process approach in order to describe patterns in cell distribution within tissue samples taken from colorectal cancer (CRC) patients. In particular, our approach is centered on the Palm intensity function. This leads to taking an approximate-likelihood technique in fitting point processes models. We consider two Neyman-Scott point processes and a void process, fitting these point process models to the CRC patient data. We find that the parameter estimates of these models may be used to quantify the spatial arrangement of cells. Importantly, we observe characteristic differences in the spatial arrangement of cells between patients who died from CRC and those alive at follow-up

Prediction of stillbirth from placental growth factor at 19-24 weeks

Objectives: To investigate whether measurement of maternal serum placental growth factor (PLGF) at 19-24 weeks’ gestation improves the performance of screening for stillbirths that is achieved by a combination of maternal factors, fetal biometry and uterine artery pulsatility index (UT-PI) and evaluate the performance of screening of this model for all stillbirths and those due to impaired placentation and unexplained or other causes. Methods: This was a prospective screening study of 70,003 singleton pregnancies including 268 stillbirths, carried out in two phases. The first phase, which included prospective measurements of UT-PI and fetal biometry were available in all cases. The second phase included prospective measurements of maternal serum PLGF which were available for 9,870 live births and 86 antepartum stillbirths. The values of PLGF obtained from this screening study were simulated in the remaining cases based on bivariate Gaussian distributions, defined by the mean and standard deviations. Multivariate logistic regression analysis was used to determine whether the addition of maternal serum PLGF improved the performance of screening that was achieved by a combination of maternal factors, fetal biometry and UT-PI. Results: Significant contribution to the prediction of stillbirths was provided by maternal factor derived a priori risk, MoM values of PLGF, UT-PI and fetal biometry Z-scores. A model combining these variables predicted 58% of all stillbirths and 84% of those due to impaired placentation, at false positive rate of 10%; within the impaired placentation group the detection rate of stillbirth at 37 weeks (97% vs 61%; p<0.01). Conclusions: A high proportion of stillbirths due to impaired placentation can be effectively identified in the second trimester of pregnancy

An integrative modelling framework for passive acoustic telemetry

The work was supported by a PhD Studentship at the University of St Andrews funded by NatureScot, via the Marine Alliance for Science and Technology for Scotland (MASTS), and the Centre for Research into Ecological and Environmental Modelling. Data were made available through the Movement Ecology of Flapper Skate project funded by NatureScot (project 015960) and Marine Scotland (projects SP004 and SP02B0). Jane Dodd, Ronnie Campbell, Roger Eaton, Francis Neat and Dmitry Aleynik supported this project. MASTS and Shark Guardian provided additional funding. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.Passive acoustic telemetry is widely used to study the movements of aquatic animals. However, a holistic, mechanistic modelling framework that permits the reconstruction of fine-scale movements and emergent patterns of space use from detections at receivers remains lacking. Here, we introduce an integrative modelling framework that recapitulates the movement and detection processes that generate detections to reconstruct fine-scale movements and patterns of space use. This framework is supported by a new family of algorithms designed for detection and depth observations and can be flexibly extended to incorporate other data types. Using simulation, we illustrate applications of our framework and evaluate algorithm utility and sensitivity in different settings. As a case study, we analyse movement data collected from the Critically Endangered flapper skate (Dipturus intermedius) in Scotland. We show that our methods can be used to reconstruct fine-scale movement paths, patterns of space use and support habitat preference analyses. For reconstructing patterns of space use, simulations show that the methods are consistently more instructive than the most widely used alternative approach (the mean-position algorithm), particularly in clustered receiver arrays. For flapper skate, the reconstruction of movements reveals responses to disturbance, fine-scale spatial partitioning and patterns of space use with significant implications for marine management. We conclude that this framework represents a widely applicable methodological advance with applications to studies of pelagic, demersal and benthic species across multiple spatiotemporal scales.Publisher PDFPeer reviewe

Careful prior specification avoids incautious inference for log-Gaussian Cox point processes

The BCI forest dynamics research project was founded by S.P. Hubbell and R.B. Foster and is now managed by R. Condit, S. Lao, and R. Perez under the Center for Tropical Forest Science and the Smithsonian Tropical Research in Panama. Numerous organizations have provided funding, principally the U.S. National Science Foundation, and hundreds of field workers have contributed. The data used can be requested and generally granted at http://ctfs.si.edudatarequest. Kriged estimates for concentration of the soil nutrients were downloaded from http://ctfs.si.edu/webatlas/datasets/bci/soilmaps/BCIsoil.html. We acknowledge the principal investigators that were responsible for collecting and analysing the soil maps (Jim Dallin, Robert John, Kyle Harms, Robert Stallard and Joe Yavitt), the funding sources (NSF DEB021104,021115, 0212284,0212818 and OISE 0314581, STRI Soils Initiative and CTFS) and field assistants (Paolo Segre and Juan Di Trani).Peer reviewedPostprin

Environmental cycles and individual variation in the vertical movements of a benthic elasmobranch

This research was supported by a PhD Studentship at the University of St Andrews, jointly funded by NatureScot via the Marine Alliance for Science and Technology for Scotland (MASTS), and the Centre for Research into Ecological and Environmental Modelling. The data were collected as part of research funded by NatureScot (project 015960) and Marine Scotland (projects SP004 and SP02B0) and the Movement Ecology of Flapper Skate (MEFS) project funded by the same organisations. Additional funding was provided from MASTS, in the form of a Small Research Grant, and Shark Guardian. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.Trends in depth and vertical activity reflect the behaviour, habitat use and habitat preferences of marine organisms. However, among elasmobranchs, research has focused heavily on pelagic sharks, while the vertical movements of benthic elasmobranchs, such as skate (Rajidae), remain understudied. In this study, the vertical movements of the Critically Endangered flapper skate (Dipturus intermedius) were investigated using archival depth data collected at 2 min intervals from 21 individuals off the west coast of Scotland (56.5°N, −5.5°W) in 2016–17. Depth records comprised nearly four million observations and included eight time series longer than 1 year, forming one of the most comprehensive datasets collected on the movement of any skate to date. Additive modelling and functional data analysis were used to investigate vertical movements in relation to environmental cycles and individual characteristics. Vertical movements were dominated by individual variation but included prolonged periods of limited activity and more extensive movements that were associated with tidal, diel, lunar and seasonal cycles. Diel patterns were strongest, with irregular but frequent movements into shallower water at night, especially in autumn and winter. This research strengthens the evidence for vertical movements in relation to environmental cycles in benthic species and demonstrates a widely applicable flexible regression framework for movement research that recognises the importance of both individual-specific and group-level variation.Publisher PDFPeer reviewe

Understanding species distribution in dynamic populations : a new approach using spatio‐temporal point process models

Funding: EU consolidator’s grant STATEMIG 310820 (SB).Understanding and predicting a species’ distribution across a landscape is of central importance in ecology, biogeography and conservation biology. However, it presents daunting challenges when populations are highly dynamic (i.e. increasing or decreasing their ranges), particularly for small populations where information about ecology and life history traits is lacking. Currently, many modelling approaches fail to distinguish whether a site is unoccupied because the available habitat is unsuitable or because a species expanding its range has not arrived at the site yet. As a result, habitat that is indeed suitable may appear unsuitable. To overcome some of these limitations, we use a statistical modelling approach based on spatio‐temporal log‐Gaussian Cox processes. These model the spatial distribution of the species across available habitat and how this distribution changes over time, relative to covariates. In addition, the model explicitly accounts for spatio‐temporal dynamics that are unaccounted for by covariates through a spatio‐temporal stochastic process. We illustrate the approach by predicting the distribution of a recently established population of Eurasian cranes Grus grus in England, UK, and estimate the effect of a reintroduction in the range expansion of the population. Our models show that wetland extent and perimeter‐to‐area ratio have a positive and negative effect, respectively, in crane colonisation probability. Moreover, we find that cranes are more likely to colonise areas near already occupied wetlands and that the colonisation process is progressing at a low rate. Finally, the reintroduction of cranes in SW England can be considered a human‐assisted long‐distance dispersal event that has increased the dispersal potential of the species along a longitudinal axis in S England. Spatio‐temporal log‐Gaussian Cox process models offer an excellent opportunity for the study of species where information on life history traits is lacking, since these are represented through the spatio‐temporal dynamics reflected in the model.PostprintPeer reviewe

An integrative modelling framework for passive acoustic telemetry

Passive acoustic telemetry is widely used to study the movements of aquatic animals. However, a holistic, mechanistic modelling framework that permits the reconstruction of fine‐scale movements and emergent patterns of space use from detections at receivers remains lacking. Here, we introduce an integrative modelling framework that recapitulates the movement and detection processes that generate detections to reconstruct fine‐scale movements and patterns of space use. This framework is supported by a new family of algorithms designed for detection and depth observations and can be flexibly extended to incorporate other data types. Using simulation, we illustrate applications of our framework and evaluate algorithm utility and sensitivity in different settings. As a case study, we analyse movement data collected from the Critically Endangered flapper skate (Dipturus intermedius) in Scotland. We show that our methods can be used to reconstruct fine‐scale movement paths, patterns of space use and support habitat preference analyses. For reconstructing patterns of space use, simulations show that the methods are consistently more instructive than the most widely used alternative approach (the mean‐position algorithm), particularly in clustered receiver arrays. For flapper skate, the reconstruction of movements reveals responses to disturbance, fine‐scale spatial partitioning and patterns of space use with significant implications for marine management. We conclude that this framework represents a widely applicable methodological advance with applications to studies of pelagic, demersal and benthic species across multiple spatiotemporal scales

Graph-based simulated annealing: a hybrid approach to stochastic modeling of complex microstructures

A stochastic model is proposed for the efficient simulation of complex three-dimensional microstructures consisting of two different phases. The model is based on a hybrid approach, where in a first step a graph model is developed using ideas from stochastic geometry. Subsequently, the microstructure model is built by applying simulated annealing to the graph model. As an example of application, the model is fitted to a tomographic image describing the microstructure of electrodes in Li-ion batteries. The goodness of model fit is validated by comparing morphological characteristics of experimental and simulated data