Ecological Risk Assessment for the Temperate Demersal Elasmobranch Resource

In March 2021, the Department of Primary Industries and Regional Development (Department) convened an ecological risk assessment (ERA) of the fisheries that access the Temperate Demersal Elasmobranch Resource (Resource). ERAs are conducted by the Department as part of its Ecosystem Based Fisheries Management framework

In vitro amplification of H-type atypical bovine spongiform encephalopathy by protein misfolding cyclic amplification

The in vitro amplification of prions by serial protein misfolding cyclic amplification has been shown to detect PrPSc to levels at least as sensitive as rodent bioassay but in a fraction of the time. Bovine spongiform encephalopathy is a zoonotic prion disease in cattle and has been shown to occur in three distinct forms, classical BSE (C-BSE) and two atypical BSE forms (L-BSE and H-BSE). Atypical forms are usually detectedin asymptomatic, older cattle and are suggested to be spontaneous forms of the disease. Here, we show the development of a serial protein misfolding cyclic amplification method for the detection of H-BSE. The assay could detect PrPSc from 3 distinct experimental isolates of H-BSE, could detect PrPSc in as little as 1 x 10-12 g of brain material and was highly specific. Additionally, the product of serial protein misfolding cyclic amplification at all dilutions of seed analysed could be readily distinguished from L-BSE, which did not amplify, and C-BSE, which had PrPSc with distinct protease K-resistance and protease K-resistant PrPSc molecular weights

Text message-based diabetes self-management support (SMS4BG): study protocol for a randomised controlled trial

BACKGROUND: Addressing the increasing prevalence, and associated disease burden, of diabetes is a priority of health services internationally. Interventions to support patients to effectively self-manage their condition have the potential to reduce the risk of costly and debilitating complications. The utilisation of mobile phones to deliver self-management support allows for patient-centred care at the frequency and intensity that patients desire from outside the clinic environment. Self-Management Support for Blood Glucose (SMS4BG) is a novel text message-based intervention for supporting people with diabetes to improve self-management behaviours and achieve better glycaemic control and is tailored to individual patient preferences, demographics, clinical characteristics, and culture. This study aims to assess whether SMS4BG can improve glycaemic control in adults with poorly controlled diabetes. This paper outlines the rationale and methods of the trial. METHODS/DESIGN: A two-arm, parallel, randomised controlled trial will be conducted across New Zealand health districts. One thousand participants will be randomised at a 1:1 ratio to receive SMS4BG, a theoretically based and individually tailored automated text message-based diabetes self-management support programme (intervention) in addition to usual care, or usual care alone (control). The primary outcome is change in glycaemic control (HbA1c) at 9 months. Secondary outcomes include glycaemic control at 3 and 6 months, self-efficacy, self-care behaviours, diabetes distress, health-related quality of life, perceived social support, and illness perceptions. Cost information and healthcare utilisation will also be collected as well as intervention satisfaction and interaction. DISCUSSION: This study will provide information on the effectiveness of a text message-based self-management support tool for people with diabetes. If found to be effective it has the potential to provide individualised support to people with diabetes across New Zealand (and internationally), thus extending care outside the clinic environment.<br /

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, reconstructing their gene trees, and taking their differences as indicators of hybridization. However, methods that follow this approach mostly ignore population effects, such as incomplete lineage sorting (ILS). Given that hybridization occurs between closely related organisms, ILS may very well be at play and, hence, must be accounted for in the analysis framework. To address this issue, we present a parsimony criterion for reconciling gene trees within the branches of a phylogenetic network, and a local search heuristic for inferring phylogenetic networks from collections of gene-tree topologies under this criterion. This framework enables phylogenetic analyses while accounting for both hybridization and ILS. Further, we propose two techniques for incorporating information about uncertainty in gene-tree estimates. Our simulation studies demonstrate the good performance of our framework in terms of identifying the location of hybridization events, as well as estimating the proportions of genes that underwent hybridization. Also, our framework shows good performance in terms of efficiency on handling large data sets in our experiments. Further, in analyzing a yeast data set, we demonstrate issues that arise when analyzing real data sets. While a probabilistic approach was recently introduced for this problem, and while parsimonious reconciliations have accuracy issues under certain settings, our parsimony framework provides a much more computationally efficient technique for this type of analysis. Our framework now allows for genome-wide scans for hybridization, while also accounting for ILS

On the accumulation of planetesimals near disc gaps created by protoplanets

We have performed three-dimensional two-fluid (gas-dust) hydrodynamical models of circumstellar discs with embedded protoplanets (3 - 333 M\oplu) and small solid bodies (radii 10cm to 10m). We find that high mass planets (\gtrsim Saturn mass) open sufficiently deep gaps in the gas disc such that the density maximum at the outer edge of the gap can very efficiently trap metre-sized solid bodies. This allows the accumulation of solids at the outer edge of the gap as solids from large radii spiral inwards to the trapping region. This process of accumulation occurs fastest for those bodies that spiral inwards most rapidly, typically metre-sized boulders, whilst smaller and larger objects will not migrate sufficiently rapidly in the discs lifetime to benefit from the process. Around a Jupiter mass planet we find that bound clumps of solid material, as large as several Earth masses, may form, potentially collapsing under self-gravity to form planets or planetesimals. These results are in agreement with Lyra et al. (2009), supporting their finding that the formation of a second generation of planetesimals or of terrestrial mass planets may be triggered by the presence of a high mass planet.Comment: 14 pages, 10 figures. Accepted for publication in MNRA

Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma

Osteosarcoma is a primary malignancy of bone that affects children and adults. Here, we present the largest sequencing study of osteosarcoma to date, comprising 112 childhood and adult tumours encompassing all major histological subtypes. A key finding of our study is the identification of mutations in insulin-like growth factor (IGF) signalling genes in 8/112 (7%) of cases. We validate this observation using fluorescence in situ hybridization (FISH) in an additional 87 osteosarcomas, with IGF1 receptor (IGF1R) amplification observed in 14% of tumours. These findings may inform patient selection in future trials of IGF1R inhibitors in osteosarcoma. Analysing patterns of mutation, we identify distinct rearrangement profiles including a process characterized by chromothripsis and amplification. This process operates recurrently at discrete genomic regions and generates driver mutations. It may represent an age-independent mutational mechanism that contributes to the development of osteosarcoma in children and adults alike

Rugby Fans in Training New Zealand (RUFIT-NZ): protocol for a randomized controlled trial to assess the effectiveness and cost-effectiveness of a healthy lifestyle program for overweight men delivered through professional rugby clubs in New Zealand

Background A healthy lifestyle program that appeals to, and supports, obese New Zealand (NZ) European, Māori (indigenous) and Pasifika men to achieve weight loss is urgently needed. In Scotland, Football Fans in Training (FFIT), a weight management and healthy lifestyle program for overweight and obese men aged 35–65 years , delivered by community coaching staff at professional football clubs, has been shown to be beneficial and cost-effective. A pilot program inspired by FFIT but delivered by professional rugby clubs in NZ (n = 96) was shown to be effective in weight loss, improved physiological outcomes, and adherence to healthy lifestyle behaviors in overweight and obese men. The objective of this trial is to determine the effectiveness and cost-effectiveness of the Rugby Fans in Training New Zealand (RUFIT-NZ) program. Methods A pragmatic, two-arm, multi-center, randomized controlled trial involving 308 overweight and obese men aged 30–65 years, randomized to either an intervention group (n = 154) or a wait-list control group (n = 154). The intervention-group participated in the 12-week RUFIT-NZ program, a gender-sensitized, healthy lifestyle intervention adapted to the environment and cultural diversity of NZ and delivered through professional rugby clubs. Participants in the intervention group undergo physical training sessions, in addition to workshop-based sessions to learn about nutrition, physical activity, sleep, sedentary behavior, and a range of behavior-change strategies for sustaining a healthier lifestyle. The control group receives the program after 52 weeks. The primary outcome is change in body weight from baseline to 52 weeks. Secondary outcomes include change in body weight at 12 weeks; waist circumference, blood pressure, fitness, and lifestyle behaviors at 12 and 52 weeks; and cost-effectiveness. A process evaluation informed by the RE-AIM framework will evaluate potential implementation of RUFIT-NZ as an ongoing program in NZ after the trial. Discussion This trial will investigate the effectiveness and cost-effectiveness of the RUFIT-NZ program in overweight and obese NZ men