Australian ticks through time and place

In the Australian small animal veterinary context, the paralysis tick Ixodes holocyclus and the brown dog tick Rhipicephalus sanguineus are the most significant ticks of medical and economic significance. Of the two, I. holocyclus is the most medically and veterinary significant tick along the eastern coastline of Australia. It is known to cause fatal and flaccid paralysis and allergic reactions in humans and animals. In regional Australia, R. sanguineus is problematic due to its endophilic nature and affinity for parasitising canids. They are known disease vectors and high tick burdens are associated with clinical anaemia. This thesis aimed to determine the effect of location and time on the small animal veterinary and medically significant ticks and their bacterial profile. Nymph ticks were retrieved from the environment in Sydney, NSW and adult ticks were retrieved from dogs in Sydney, and regional NSW. A systematic survey was completed to provide an update to the current identity of ticks in metropolitan Sydney, and regional NSW via morphological and molecular means. Next generation sequencing (NGS) technology was used to determine the microbiota of I. holocyclus and whether it differs between life stages and location in NSW. The microbial diversity of I. holocyclus across various localities in NSW was established using a NGS approach for nymph and adult I. holocyclus at various locations along the eastern coastline of NSW. To investigate the identity and distribution of brown dog ticks across Australia, a systematic survey was conducted to determine the current distribution. Further, due to the ambiguity surrounding the morphology of brown dog ticks, it was necessary to determine their genetic identity in Australia. As brown dog ticks were first described in Australia in 1896, a retrospective study was conducted on Australian museum material of “R. sanguineus”, allowing for the confirmation of the past and present identities of brown dog ticks across Australia

Cross-cutting principles for planetary health education

Since the 2015 launch of the Rockefeller Foundation Lancet Commission on planetary health,1 an enormous groundswell of interest in planetary health education has emerged across many disciplines, institutions, and geographical regions. Advancing these global efforts in planetary health education will equip the next generation of scholars to address crucial questions in this emerging field and support the development of a community of practice. To provide a foundation for the growing interest and efforts in this field, the Planetary Health Alliance has facilitated the first attempt to create a set of principles for planetary health education that intersect education at all levels, across all scales, and in all regions of the world—ie, a set of cross-cutting principles

Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects

Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Generalized Hilbert-Huang Transform with Applications

Power system dynamic processes may exhibit highly complex spatial and temporal dynamics and take place over a great range of timescales. When frequency analysis requires the separation of a signal into its essential components,resolution becomes an important issue. The Hilbert–Huang transform (HHT) introduced by Huang is a powerful data-driven, adaptive technique for analyzing data from nonlinear and nonstationary processes. The core to thisdevelopment is the empirical mode decomposition (EMD) that separates a signal into a series of amplitude- and frequency-modulated signal components from which temporal modal properties can be derived. Previous analytical works have shown that several problems may prevent the effective use of EMD on various types of signals especially those exhibiting closely spaced frequency components and mode mixing. The method allows a precise characterization of temporal modal frequency and damping behavior and enables a better interpretation of nonlinear and nonstationary phenomena in physical terms.This chapter investigates several extension to the HHT. A critical review of existing approaches to HHT is first presented. Then, a refined masking signal EMD method is introduced that overcomes some of the limitations of theexisting approaches to isolate and extract modal components. Techniques to compute a local Hilbert transformation are discussed and a number of numericalissues are discussed.As case studies, the applications of the various EDM algorithms in power systems’ signal analysis are presented. The focus of the case studies is to accurately characterize composite system oscillation in a wide-area power network

Reptile-associated Borrelia species in the goanna tick (Bothriocroton undatum) from Sydney, Australia

Abstract Background Knowledge on the capacity of Australian ticks to carry Borrelia species is currently limited or missing. To evaluate the potential of ticks to carry bacterial pathogens and their DNA, it is imperative to have a robust workflow that maximises recovery of bacterial DNA within ticks in order to enable accurate identification. By exploiting the bilateral anatomical symmetry of ticks, we were able to directly compare two DNA extraction methods for 16S rRNA gene diversity profiling and pathogen detection. We aimed to assess which combination of DNA extraction and 16S rRNA hypervariable region enables identification of the greatest bacterial diversity, whilst minimising bias, and providing the greatest capacity for the identification of Borrelia spp. Results We collected Australian endemic ticks (Bothriocroton undatum), isolated DNA from equal tick halves using two commercial DNA extraction methods and sequenced samples using V1-V3 and V3-V4 16S rRNA gene diversity profiling assays. Two distinct Borrelia spp. operational taxonomic units (OTUs) were detected using the V1-V3 16S rRNA hypervariable region and matching Borrelia spp. sequences were obtained using a conventional nested-PCR. The tick 16S rRNA gene diversity profile was dominated by Rickettsia spp. (98–99%), while the remaining OTUs belonged to Proteobacteria (51–81%), Actinobacteria (6–30%) and Firmicutes (2–7%). Multiple comparisons tests demonstrated biases in each of the DNA extraction kits towards different bacterial taxa. Conclusions Two distinct Borrelia species belonging to the reptile-associated Borrelia group were identified. Our results show that the method of DNA extraction can promote bias in the final microbiota identified. We determined an optimal DNA extraction method and 16S rRNA gene diversity profile assay that maximises detection of Borrelia species

Short-term comparison between extended depth-of-focus prototype contact lenses and a commercially-available center-near multifocal

Purpose: To compare the visual performance of prototype contact lenses which extend depth-of-focus (EDOF) by deliberate manipulation of multiple higher-order spherical aberration terms and a commercially-available center-near lens (AIR OPTIX Aqua Multifocal, AOMF). Methods: This was a prospective, cross-over, randomized, single-masked (participant), short-term clinical trial where 52 participants (age 45–70 years) were stratified as low, medium or high presbyopes and wore EDOF and AOMF on different days. Objective measures comprised high and low contrast visual acuity (HCVA/LCVA, log MAR), and contrast sensitivity (log units) at 6 m; HCVA at 70 cm, 50 cm and 40 cm and stereopsis (seconds of arc) at 40 cm. HCVA at 70 cm, 50 cm and 40 cm were measured as “comfortable acuity” rather than conventional resolution acuity. Subjective measures comprised clarity-of-vision and ghosting at distance, intermediate and near, overall vision satisfaction and ocular comfort (1–10 numeric rating scale) and lens purchase (yes/no response). Statistical analysis included repeated measures ANOVA, paired t-tests and McNemar's test. Results: Significant differences between lens types were independent of strata (p ≥ 0.119). EDOF was significantly better than AOMF for HCVA at 40 cm (0.42 ± 0.18 vs. 0.48 ± 0.22, p = 0.024), stereopsis (98 ± 88 vs. 141 ± 114, p < 0.001), clarity-of-vision at intermediate (8.5 ± 1.6 vs. 7.7 ± 1.9, p = 0.006) and near (7.3 ± 2.5 vs. 6.2 ± 2.5, p = 0.005), lack-of-ghosting (p = 0.012), overall vision satisfaction (7.5 ± 1.7 vs. 6.4 ± 2.2, p < 0.001) and ocular comfort (9.0 ± 1.0 vs. 8.3 ± 1.7, p = 0.002). Significantly more participants chose to only-purchase EDOF (33% vs. 6%, p = 0.003).). There were no significant differences between lens types for any objective measure at 6 m or clarity-of-vision at distance (p ≥ 0.356). Conclusions: EDOF provides better intermediate and near vision performance in presbyopes than AOMF with no difference for distance vision during short-term wear

Additional file 1: Table S1. of Reptile-associated Borrelia species in the goanna tick (Bothriocroton undatum) from Sydney, Australia

Summary of tick samples used. Table S2. Summary of Qubit DNA concentrations and qPCR bacterial numbers estimates. Table S3. Summary of DNA sequencing of bacterial 16S rRNA gene. (XLSX 18 kb

SABRes: A tool for in silico detection of drug resistance conferring mutations in SARS-CoV-2 genomes

The emergence of resistance to antiviral drugs increasingly used to treat SARS-CoV-2 infections has been recognised as a significant threat to COVID-19 control. In addition, some SARS-CoV-2 variants of concern appear to be intrinsically resistant to several classes of these antiviral agents. Therefore, there is a critical need for rapid recognition of clinically relevant polymorphisms in SARS-CoV-2 genomes associated with significant reduction of drug activity in virus neutralisation experiments. Here we present SABRes, a bioinformatic tool, which leverages on expanding public datasets of SARS-CoV-2 genomes and allows detection of drug resistance mutations in consensus genomes as well as in viral subpopulations. We have applied SABRes to detect resistance-conferring mutations in over 25,000 genomes generated over the course of the SARS-CoV-2 pandemic in Australia