Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures

In this article we propose novel Bayesian nonparametric methods using Dirichlet Process Mixture (DPM) models for detecting pairwise dependence between random variables while accounting for uncertainty in the form of the underlying distributions. A key criteria is that the procedures should scale to large data sets. In this regard we find that the formal calculation of the Bayes factor for a dependent-vs.-independent DPM joint probability measure is not feasible computationally. To address this we present Bayesian diagnostic measures for characterising evidence against a “null model” of pairwise independence. In simulation studies, as well as for a real data analysis, we show that our approach provides a useful tool for the exploratory nonparametric Bayesian analysis of large multivariate data sets

Low-dimensional dynamical system model for observed coherent structures in ocean satellite data

The dynamics of coherent structures present in real-world environmental data is analyzed. The method developed in this Paper combines the power of the Proper Orthogonal Decomposition (POD) technique to identify these coherent structures in experimental data sets, and its optimality in providing Galerkin basis for projecting and reducing complex dynamical models. The POD basis used is the one obtained from the experimental data. We apply the procedure to analyze coherent structures in an oceanic setting, the ones arising from instabilities of the Algerian current, in the western Mediterranean Sea. Data are from satellite altimetry providing Sea Surface Height, and the model is a two-layer quasigeostrophic system. A four-dimensional dynamical system is obtained that correctly describe the observed coherent structures (moving eddies). Finally, a bifurcation analysis is performed on the reduced model.Comment: 23 pages, 7 figure

Exploring the socioethical dilemmas in the use of a global health archive

A global health archive consisting of podoconiosis tissue slides and blocks (which was collected and imported into the UK before the introduction of the Human Tissue Act), was donated to Brighton & Sussex Medical School in 2014. There is little guidance on the socioethical and legal issues surrounding the retrospective use of archived or ‘abandoned’ tissue samples, which poses a number of questions relating to the ethical standing of the archive. There is a great deal of interpretation in the guidelines that are currently in existence, however modern ethical principles cannot be applied as it is not feasible to either reconsent or retrospectively seek approval. Our research team believed that it was unethical to leave the archive in storage, as this option favours neither researcher nor subjects. Permission was obtained from the Human Tissue Authority and a local ethics board for the tissues to be utilised in on-going research on podoconiosis aetiology. There is a delicate balance between the benefits gained by society relating to the development and progress of scientific research and the risks to the donor regarding the reuse of their tissues. Clearer guidelines should be made available to ensure that researchers are able to re-use tissue archives in contemporary research

Vascularization of the dorsal root ganglia and peripheral nerve of the mouse: Implications for chemical-induced peripheral sensory neuropathies

Although a variety of industrial chemicals, as well as several chemotherapeutic agents used to treat cancer or HIV, preferentially induce a peripheral sensory neuropathy what remains unclear is why these agents induce a sensory vs. a motor or mixed neuropathy. Previous studies have shown that the endothelial cells that vascularize the dorsal root ganglion (DRG), which houses the primary afferent sensory neurons, are unique in that they have large fenestrations and are permeable to a variety of low and high molecular weight agents. In the present report we used whole-mount preparations, immunohistochemistry, and confocal laser scanning microscopy to show that the cell body-rich area of the L4 mouse DRG has a 7 fold higher density of CD31+ capillaries than cell fiber rich area of the DRG or the distal or proximal aspect of the sciatic nerve. This dense vascularization, coupled with the high permeability of these capillaries, may synergistically contribute, and in part explain, why many potentially neurotoxic agents preferentially accumulate and injure cells within the DRG. Currently, cancer survivors and HIV patients constitute the largest and most rapidly expanding groups that have chemically induced peripheral sensory neuropathy. Understanding the unique aspects of the vascularization of the DRG and closing the endothelial fenestrations of the rich vascular bed of capillaries that vascularize the DRG before intravenous administration of anti-neoplastic or anti-HIV therapies, may offer a mechanism based approach to attenuate these chemically induced peripheral neuropathies in these patients

Limiting behaviour of Fréchet means in the space of phylogenetic trees

As demonstrated in our previous work on T4, the space of phylogenetic trees with four leaves, the topological structure of the space plays an important role in the non-classical limiting behaviour of the sample Fréchet means in T4. Nevertheless, the techniques used in that paper cannot be adapted to analyse Fréchet means in the space Tm of phylogenetic trees with m(⩾5)m(⩾5) leaves. To investigate the latter, this paper first studies the log map of Tm. Then, in terms of a modified version of this map, we characterise Fréchet means in Tm that lie in top-dimensional or co-dimension one strata. We derive the limiting distributions for the corresponding sample Fréchet means, generalising our previous results. In particular, the results show that, although they are related to the Gaussian distribution, the forms taken by the limiting distributions depend on the co-dimensions of the strata in which the Fréchet means lie

STAR-loc: Dataset for STereo And Range-based localization

This document contains a detailed description of the STAR-loc dataset. For a quick starting guide please refer to the associated Github repository (https://github.com/utiasASRL/starloc). The dataset consists of stereo camera data (rectified/raw images and inertial measurement unit measurements) and ultra-wideband (UWB) data (range measurements) collected on a sensor rig in a Vicon motion capture arena. The UWB anchors and visual landmarks (Apriltags) are of known position, so the dataset can be used for both localization and Simultaneous Localization and Mapping (SLAM).Comment: 15 pages, 15 figure

Role of human milk oligosaccharides in Group B Streptococcus colonisation.

Group B Streptococcus (GBS) infection is a major cause of morbidity and mortality in infants. The major risk factor for GBS disease is maternal and subsequent infant colonisation. It is unknown whether human milk oligosaccharides (HMOs) protect against GBS colonisation. HMO production is genetically determined and linked to the Lewis antigen system. We aimed to investigate the association between HMOs and infant GBS colonisation between birth and postnatal day 90. Rectovaginal swabs were collected at delivery, as well as colostrum/breast milk, infant nasopharyngeal and rectal swabs at birth, 6 days and days 60-89 postpartum from 183 Gambian mother/infant pairs. GBS colonisation and serotypes were determined using culture and PCR. (1)H nuclear magnetic resonance spectroscopy was used to characterise the mother's Lewis status and HMO profile in breast milk. Mothers who were Lewis-positive were significantly less likely to be colonised by GBS (X (2)=12.50, P<0.001). Infants of Lewis-positive mothers were less likely GBS colonised at birth (X (2)=4.88 P=0.03) and more likely to clear colonisation between birth and days 60-89 than infants born to Lewis-negative women (P=0.05). There was no association between Secretor status and GBS colonisation. In vitro work revealed that lacto-N-difucohexaose I (LNDFHI) correlated with a reduction in the growth of GBS. Our results suggest that HMO such as LNDFHI may be a useful adjunct in reducing maternal and infant colonisation and hence invasive GBS disease. Secretor status offers utility as a stratification variable in GBS clinical trials

Engaging with assessment: increasing student engagement through continuous assessment

Student engagement is intrinsically linked to two important metrics in learning: student satisfaction and the quality of the student experience. One of the ways that engagement can be influenced is through careful curriculum design. Using the knowledge that many students are ‘assessment-driven’ a low stakes continuous weekly summative e-assessment was introduced to a module. The impact this had on student engagement was measured by studying student activity within the module virtual learning environment (VLE). It was found that introduction of the e-assessments led to a significant increase in VLE activity compared to the VLE activity in that module the previous year, and also compared to the VLE activity of two other modules studied by the same student cohort. As many institutions move towards greater blended or online deliveries it will become more important to ensure that VLEs encourage high levels of student engagement in order to maintain or enhance the student experience. Keywords : continuous assessment, learning analytics, student engagement, virtual learning environment