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"Austin, Andrew"
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Across the Indian Ocean: A remarkable example of trans-oceanic dispersal in an austral mygalomorph spider
The Migidae are a family of austral trapdoor spiders known to show a highly restricted and disjunct distribution pattern. Here, we aim to investigate the phylogeny and historical biogeography of the group, which was previously thought to be vicariant in origin, and examine the biogeographic origins of the genus Moggridgea using a dated multi-gene phylogeny. Moggridgea specimens were sampled from southern Australia and Africa, and Bertmainus was sampled from Western Australia. Sanger sequencing methods were used to generate a robust six marker molecular dataset consisting of the nuclear genes 18S rRNA, 28S rRNA, ITS rRNA, XPNPEP3 and H3 and the mitochondrial gene COI. Bayesian and Maximum Likelihood methods were used to analyse the dataset, and the key dispersal nodes were dated using BEAST. Based on our data, we demonstrate that Moggridgea rainbowi from Kangaroo Island, Australia is a valid member of the otherwise African genus Moggridgea. Molecular clock dating analyses show that the inter-specific divergence of M. rainbowi from African congeners is between 2.27-16.02 million years ago (Mya). This divergence date significantly post-dates the separation of Africa from Gondwana (95 Mya) and therefore does not support a vicariant origin for Australian Moggridgea. It also pre-dates human colonisation of Kangaroo Island, a result which is further supported by the intra-specific divergence date of 1.10-6.39 Mya between separate populations on Kangaroo Island. These analyses provide strong support for the hypothesis that Moggridgea colonised Australia via long-distance trans-Indian Ocean dispersal, representing the first such documented case in a mygalomorph spider.
Journal Article
Prednisolone or Pentoxifylline for Alcoholic Hepatitis
In this randomized trial in patients hospitalized with alcoholic hepatitis, pentoxifylline did not improve survival. The 28-day survival advantage in patients treated with prednisolone did not reach significance and was not sustained at 90 days or 1 year.
Alcoholic hepatitis is a distinct manifestation of alcoholic liver disease that is characterized by jaundice and liver failure. This condition develops in persons with a history of prolonged and heavy alcohol use.
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The severity of alcoholic hepatitis is conventionally defined by Maddrey’s discriminant function, which is calculated as 4.6×(patient’s prothrombin time in seconds−control’s prothrombin time in seconds)+patient’s serum bilirubin level in milligrams per deciliter; a value of 32 or higher indicates severe alcoholic hepatitis that carries an adverse prognosis, with mortality of 20 to 30% within 1 month after presentation and 30 to 40% within 6 months after presentation.
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Journal Article
Baseband and RF hardware impairments in full-duplex wireless systems: experimental characterisation and suppression
Hardware imperfections can significantly reduce the performance of full-duplex wireless systems by introducing non-idealities and random effects that make it challenging to fully suppress self-interference. Previous research has mostly focused on analysing the impact of hardware imperfections on full-duplex systems, based on simulations and theoretical models. In this paper, we follow a measurement-based approach to experimentally identify and isolate these hardware imperfections leading to residual self-interference in full-duplex nodes. Our measurements show the important role of images arising from in-phase and quadrature (IQ) imbalance in the transmitter and receiver mixers. We also observe baseband non-linearities in the digital-to-analog converters (DAC), which can introduce strong harmonic components in the transmitted signal that have not been considered previously. A corresponding general mathematical model to suppress these components of the self-interference signal arising from the hardware non-idealities is developed from the observations and measurements. Results from a 10 MHz bandwidth full-duplex system, operating at 2.48 GHz, show that up to 13 dB additional suppression, relative to state-of-the-art implementations, can be achieved by jointly compensating for IQ imbalance and DAC non-linearities.
Journal Article
Long range wide area network for agricultural wireless underground sensor networks
Wireless underground sensor networks (WUSNs) enable large-scale agricultural monitoring for improving farming efficiency and reducing pollution. A WUSN system based on the long range wide area network (LoRaWAN) standard is proposed. A novel LoRaWAN-based simulator is developed to model wireless signal attenuation and path loss in an underground environment by incorporating the Peplinski and modified Friis models. The simulator incorporates the full network stack of the LoRa physical and MAC layers. Simulation results show LoRaWAN-based WUSNs (with a node burial depth of 50 cm) can maintain network connectivity with a range of over several kilometres. The simulation results also show the regional duty cycle restriction significantly reduces network scalability due to acknowledgements from end-devices. For agricultural applications where such frequent acknowledgements are not required, the results show a LoRaWAN WUSN is scalable. A field experiment to evaluate the accuracy of the theoretical path loss model was conducted and results were found to agree with the simulations.
Journal Article
Evidence for speciation underground in diving beetles (Dytiscidae) from a subterranean archipelago
Most subterranean animals are assumed to have evolved from surface ancestors following colonization of a cave system; however, very few studies have raised the possibility of “subterranean speciation” in underground habitats (i.e., obligate cave-dwelling organisms [troglobionts] descended from troglobiotic ancestors). Numerous endemic subterranean diving beetle species from spatially discrete calcrete aquifers in Western Australia (stygobionts) have evolved independently from surface ancestors; however, several cases of sympatric sister species raise the possibility of subterranean speciation. We tested this hypothesis using vision (phototransduction) genes that are evolving under neutral processes in subterranean species and purifying selection in surface species. Using sequence data from 32 subterranean and five surface species in the genus Paroster (Dytiscidae), we identified deleterious mutations in long wavelength opsin (lwop), arrestin 1 (arr1), and arrestin 2 (arr2) shared by a sympatric sister-species triplet, arr1 shared by a sympatric sister-species pair, and lwop and arr2 shared among closely related species in adjacent calcrete aquifers. In all cases, a common ancestor possessed the function-altering mutations, implying they were already adapted to aphotic environments. Our study represents one of the first confirmed cases of subterranean speciation in cave insects. The assessment of genes undergoing pseudogenization provides a novel way of testing modes of speciation and the history of diversification in blind cave animals.
Journal Article
Distribution and Diversity of Soil Microfauna from East Antarctica: Assessing the Link between Biotic and Abiotic Factors
Terrestrial life in Antarctica has been described as some of the simplest on the planet, and mainly confined to soil microfaunal communities. Studies have suggested that the lack of diversity is due to extreme environmental conditions and thought to be driven by abiotic factors. In this study we investigated soil microfauna composition, abundance, and distribution in East Antarctica, and assessed correlations with soil geochemistry and environmental variables. We examined 109 soil samples from a wide range of ice-free habitats, spanning 2000 km from Framnes Mountains to Bailey Peninsula. Microfauna across all samples were patchily distributed, from complete absence of invertebrates to over 1600 specimens/gram of dry weight of soil (gdw), with highest microfauna abundance observed in samples with visible vegetation. Bdelloid rotifers were on average the most widespread found in 87% of sampled sites and the most abundant (44 specimens/gdw). Tardigrades occurred in 57% of the sampled sites with an abundance of 12 specimens/gdw. Nematodes occurred in 71% of samples with a total abundance of 3 specimens/gdw. Ciliates and mites were rarely found in soil samples, with an average abundance of 1.3 and 0.04 specimens/gdw, respectively. We found that microfaunal composition and abundance were mostly correlated with the soil geochemical parameters; phosphorus, NO3 (-) and salinity, and likely to be the result of soil properties and historic landscape formation and alteration, rather than the geographic region they were sampled from. Studies focusing on Antarctic biodiversity must take into account soil geochemical and environmental factors that influence population and species heterogeneity.
Journal Article
Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus)
Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly diverse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short (<100 bp) and longer (>300 bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple samples prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies.
Journal Article
Detection of the rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments
The blind cave eel, Ophisternon candidum (Mees in J R Soc West Aust 45: 24–32,1962), is a rare groundwater inhabitant found in geographically isolated populations of north-west Australia. The species is listed as vulnerable under Commonwealth legislation and is a priority consideration when environmental disturbance by resource companies is proposed. Detection of this species for Environmental Impact Assessment (EIA) and monitoring is difficult because individuals are naturally rare or traditional sampling techniques are ineffective. To properly manage the species, information on population distribution and connectivity is critical. We sought to examine whether environmental DNA (eDNA) of O. candidum could be detected and whether positive detection was correlated with previous locations where the species had been physically caught. We developed new eDNA species-specific PCR assays to screen groundwater sampling points and we detected O. candidum DNA in three boreholes where the species has previously been collected and five additional groundwater sampling points. Our results demonstrated that the newly designed assays were effective for detecting this rare and vulnerable subterranean species. This work sets a benchmark for the application of eDNA species-specific PCR assays for EIA and monitoring, and has potential for these assays to be expanded more broadly to high-throughput eDNA metabarcoding for subterranean groundwater communities in the future.
Journal Article
Coexistence of Minicircular and a Highly Rearranged mtDNA Molecule Suggests That Recombination Shapes Mitochondrial Genome Organization
Recombination has been proposed as a possible mechanism to explain mitochondrial (mt) gene rearrangements, although the issue of whether mtDNA recombination occurs in animals has been controversial. In this study, we sequenced the entire mt genome of the megaspilid wasp Conostigmus sp., which possessed a highly rearranged mt genome. The sequence of the A+T-rich region contained a number of different types of repeats, similar to those reported previously in the nematode Meloidogyne javanica, in which recombination was discovered. In Conostigmus, we detected the end products of recombination: a range of minicircles. However, using isolated (cloned) fragments of the A+T-rich region, we established that some of these minicircles were found to be polymerase chain reaction (PCR) artifacts. It appears that regions with repeats are prone to PCR template switching or PCR jumping. Nevertheless, there is strong evidence that one minicircle is real, as amplification primers that straddle the putative breakpoint junction produce a single strong amplicon from genomic DNA but not from the cloned A+T-rich region. The results provide support for the direct link between recombination and mt gene rearrangement. Furthermore, we developed a model of recombination which is important for our understanding of mtDNA evolution.
Journal Article