Fidelity of hyperbolic space for Bayesian phylogenetic inference.

Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. However, Bayesian phylogenetics faces the challenging computational problem of moving throughout the high-dimensional space of trees. Fortunately, hyperbolic space offers a low dimensional representation of tree-like data. In this paper, we embed genomic sequences as points in hyperbolic space and perform hyperbolic Markov Chain Monte Carlo for Bayesian inference in this space. The posterior probability of an embedding is computed by decoding a neighbour-joining tree from the embedding locations of the sequences. We empirically demonstrate the fidelity of this method on eight data sets. We systematically investigated the effect of embedding dimension and hyperbolic curvature on the performance in these data sets. The sampled posterior distribution recovers the splits and branch lengths to a high degree over a range of curvatures and dimensions. We systematically investigated the effects of the embedding space's curvature and dimension on the Markov Chain's performance, demonstrating the suitability of hyperbolic space for phylogenetic inference.

Inertial Force Transmission in Dense Granular Flows.

Dense granular flows are well described by several continuum models; however, their internal dynamics remain elusive. This study explores the contact force distributions in simulated steady and homogenous shear flows. The results demonstrate the existence of high magnitude contact forces in faster flows with stiffer grains. A proposed physical mechanism explains this rate-dependent force transmission. This analysis establishes a relation between contact forces and grain velocities, providing an entry point to unify a range of continuum models derived from either contact forces or grain velocity.

Shear-induced diffusion in dense granular fluids.

Granular materials are comprised of solid, athermal grains. Whilst immune to thermal motion, these grains move and diffuse when they undergo shear deformation. Here we introduce this process of shear-induced diffusion with a focus on dense flows. The goal is to present the established scaling laws for continuum diffusivity and to relate them to the micro-mechanisms of a granular random walk. We then suggest how this knowledge may help advance our understanding of granular rheology and diffusion in other soft-materials.

Viscosity of cohesive granular flows.

Cohesive granular materials such as wet sand, snow, and powders can flow like a viscous liquid. However, the elementary mechanisms of momentum transport in such athermal particulate fluids are elusive. As a result, existing models for cohesive granular viscosity remain phenomenological and debated. Here we use discrete element simulations of plane shear flows to measure the viscosity of cohesive granular materials, while tuning the intensity of inter-particle adhesion. We establish that two adhesion-related, dimensionless numbers control their viscosity. These numbers compare the force and energy required to break a bond to the characteristic stress and kinetic energy in the flow. This progresses the commonly accepted view that only one dimensionless number could control the effect of adhesion. The resulting scaling law captures strong, non-Newtonian variations in viscosity, unifying several existing viscosity models. We then directly link these variations in viscosity to adhesion-induced modifications in the flow micro-structure and contact network. This analysis reveals the existence of two modes of momentum transport, involving either grain micro-acceleration or balanced contact forces, and shows that adhesion only affects the latter. This advances our understanding of rheological models for granular materials and other soft materials such as emulsions and suspensions, which may also involve inter-particle adhesive forces.

Differentiable phylogenetics via hyperbolic embeddings with Dodonaphy.

Motivation: Navigating the high dimensional space of discrete trees for phylogenetics presents a challenging problem for tree optimization. To address this, hyperbolic embeddings of trees offer a promising approach to encoding trees efficiently in continuous spaces. However, they require a differentiable tree decoder to optimize the phylogenetic likelihood. We present soft-NJ, a differentiable version of neighbour joining that enables gradient-based optimization over the space of trees. Results: We illustrate the potential for differentiable optimization over tree space for maximum likelihood inference. We then perform variational Bayesian phylogenetics by optimizing embedding distributions in hyperbolic space. We compare the performance of this approximation technique on eight benchmark datasets to state-of-the-art methods. Results indicate that, while this technique is not immune from local optima, it opens a plethora of powerful and parametrically efficient approach to phylogenetics via tree embeddings. Availability and implementation: Dodonaphy is freely available on the web at https://www.github.com/mattapow/dodonaphy. It includes an implementation of soft-NJ.

Characteristics and outcomes of patients receiving review requests for pre-medical emergency team deterioration: a cohort study.

Objective The aim of this study was to describe the epidemiology of pre-medical emergency team (pre-MET) reviews, including patient characteristics, the frequency and nature of triggers and interventions and in-hospital outcomes. Methods An exploratory retrospective cohort study was performed using a medical record audit. Fifty orthopaedic and general medicine patients at a hospital in Melbourne, Australia, with requests for pre-MET reviews in 2016 were included. Descriptive analyses were performed. Results The median patient age was 80 years (interquartile range 19 years). Most patients were female (64%), general medical patients (82%), with limitation of medical treatment orders (52%) and modified pre-MET triggers (42%). Documented pre-MET reviews occurred for 68% of requests. Tachypnoea (24%) and staff worry (24%) were the most common pre-MET triggers. One-third of patients received two clinical interventions. One in five patients had repeat requests for a pre-MET review within 12 h. In-hospital mortality was 12%. Conclusions Most requests for pre-MET reviews related to older female patients. Clinician adherence to pre-MET policy was variable. Multicentre studies are needed to inform improvements to pre-MET strategies. What is known about the topic? Australian hospitals have introduced multi-tiered rapid response systems (RRSs) that consist of pre-MET review to comply with accreditation standards. Pre-MET reviews are triggered by early signs of clinical deterioration and are provided by admitting medical teams or senior nurses. There is limited understanding of the characteristics and outcomes of patients receiving pre-MET reviews for early clinical deterioration. What does this paper add? In a cohort of orthopaedic and general medicine patients, most patients receiving requests for pre-MET reviews were older, female medical patients, with existing modifications to pre-MET triggers. Most requests for pre-MET review were for tachypnoea or staff worry; the latter included clinical problems not addressed by predefined organisational triggers. One in five patients continued to deteriorate within 12 h of the pre-MET request. Clinician adherence to pre-MET policy varied. What are the implications for practitioners? Patients in this study frequently deteriorated in ways that did not breach predefined pre-MET triggers, demonstrating that pre-MET requests are made for a range of clinical concerns. Doctors and nurses must be vigilant for ongoing clinical deterioration in patients receiving requests for pre-MET reviews. Reflecting the timing of the recent introduction of the pre-MET review system, variable adherence to pre-MET policy raises questions about clinicians' awareness of and responsibilities in this RRS tier, the impact of workloads on RRS response capability and the suitability of existing escalation policies. Evaluation of the implementation of pre-MET review is warranted.

Two mechanisms of momentum transfer in granular flows.

This Rapid Communication highlights the physical processes at the origin of the constitutive law of dense granular flows. In simulated plane shear flows, we present a micro-mechanical expression for the phenomenological friction law µ(I). The expression highlights two distinct pathways for momentum transport-through either balanced contact forces or grain micro-acceleration. We show that these two rate-dependent processes control and explain the friction law. This understanding may help advance rheological models for granular materials and other soft materials such as emulsions and suspensions.