Cryobiopsy with radial-endobronchial ultrasound (Cryo-Radial) has comparable diagnostic yield with higher safety in comparison to computed tomography-guided transthoracic biopsy for peripheral pulmonary lesions: An exploratory randomised study.

BACKGROUND: Computed tomography-guided transthoracic biopsy (CT-TTB) is the 'gold standard' biopsy for lung nodules. Radial-endobronchial ultrasound (R-EBUS) bronchoscopy is another recommended biopsy but carries a lower diagnostic yield. Addition of cryobiopsy with R-EBUS (Cryo-Radial) has shown promising results. There are no studies comparing CT-TTB with Cryo-Radial biopsy. AIM: The co-primary aims were the diagnostic yeild and safety. The secondary aim: ability to test epidermal growth factor receptor (EGFR). METHODS: A randomised controlled, multicentre exploratory study was conducted at three tertiary hospitals. Patients with nodules >1 cm on CT of the chest were randomised to CT-TTB or Cryo-Radial. With Cryo-Radial, patients had 1-3 cryo-biopsies in addition to at least one R-EBUS biopsy through the 2.6 mm guide sheath. RESULTS: Forty-eight patients were randomised: 22 to CT-TTB and 26 to Cryo-Radial. Sixteen in the CT-TTB and 20 in the Cryo-Radial received the allocated biopsy. The diagnostic yield was CT-TTB 93.8% (15/16) versus Cryo-Radial 85% (17/20) P = 0.61 and the odds ratio was 0.37. For 5/13 (38%), a diagnosis was solely made on cryobiopsy. Eleven (78%) of 14 in CT-TTB versus 7/10 (70%) Cryo-Radial were suitable for EGFR testing P = 0.66, with odds ratio 0.63. Pneumothorax occurrence was 44% (7/16) in CT-TTB versus 4.2% (1/24) in Cryo-Radial. Two (12.5%) of 16 CT-TTB required chest drain insertion. CONCLUSION: Cryo-Radial is comparable in diagnostic yield and ability to perform EGFR testing with a significantly lower risk of pneumothorax, compared with CT-TTB. Cryo-Radial has the additional advantage of mediastinal staging during the same procedure with Linear-EBUS and is a promising first-line tool in the diagnostic method of lung cancer.

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes.

BACKGROUND: The genetic basis of wing development has been well characterised for model insect species, but remains poorly understood in phylogenetically divergent, non-model taxa. Wing-polymorphic insect species potentially provide ideal systems for unravelling the genetic basis of secondary wing reduction. Stoneflies (Plecoptera) represent an anciently derived insect assemblage for which the genetic basis of wing polymorphism remains unclear. We undertake quantitative RNA-seq of sympatric full-winged versus vestigial-winged nymphs of a widespread wing-dimorphic New Zealand stonefly, Zelandoperla fenestrata, to identify genes potentially involved in wing development and secondary wing loss. RESULTS: Our analysis reveals substantial differential expression of wing-development genes between full-winged versus vestigial-winged stonefly ecotypes. Specifically, of 23 clusters showing significant similarity to Drosophila wing development-related genes and their pea aphid orthologues, nine were significantly upregulated in full-winged stonefly ecotypes, whereas only one cluster (teashirt) was substantially upregulated in the vestigial-winged ecotype. CONCLUSIONS: These findings suggest remarkable conservation of key wing-development pathways throughout 400 Ma of insect evolution. The finding that two Juvenile Hormone pathway clusters were significantly upregulated in vestigial-winged Zelandoperla supports the hypothesis that Juvenile Hormone may play a key role in modulating insect wing polymorphism, as has previously been suggested for other insect lineages.

Genomics detects population structure within and between ocean basins in a circumpolar seabird: The white-chinned petrel.

The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (Procellaria aequinoctialis) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and first domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.

Ecological gradients drive insect wing loss and speciation: The role of the alpine treeline.

Alpine ecosystems are frequently characterized by an abundance of wing-reduced insect species, but the drivers of this biodiversity remain poorly understood. Insect wing reduction in these environments has variously been attributed to altitude, temperature, isolation, habitat stability or decreased habitat size. We used fine-scale ecotypic and genomic analyses, along with broad-scale distributional analyses of ecotypes, to unravel the ecological drivers of wing reduction in the wing-dimorphic stonefly Zelandoperla fenestrata complex. Altitudinal transects within populations revealed dramatic wing reduction over very fine spatial scales, tightly linked to the alpine treeline. Broad biogeographical analyses confirm that the treeline has a much stronger effect on these ecotype distributions than altitude per se. Molecular analyses revealed parallel genomic divergence between vestigial-winged (high altitude) and full-winged (low altitude) ecotypes across distinct streams. These data thus highlight the role of the alpine treeline as a key driver of rapid speciation, providing a new model for ecological diversification along exposure gradients.

Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls (Larus bulleri).

Black-billed gulls (Larus bulleri) are endemic to New Zealand and are suspected to be undergoing substantial population declines. They primarily breed on open gravel beds in braided rivers of the South Island-a habitat that is diminishing and becoming increasingly modified. Although management of this species is increasing, little has been published on their movements and demographics. In this study, both mitochondrial DNA (mtDNA) control region domain I and nuclear single nucleotide polymorphisms (SNPs) were examined to help understand the connectivity and population structure of black-billed gulls across the country and to help inform management decisions. Mitochondrial DNA showed no population structure, with high haplotype and low nucleotide diversity, and analyses highlighted mitochondrial introgression with the closely related red-billed gulls (Larus novaehollandiae scopulinus). Nuclear DNA analyses, however, identified two groups, with Rotorua birds in the North Island being distinct from the rest of New Zealand, and isolation-by-distance evident across the South Island populations. Gene flow primarily occurs between nearby colonies with a stepwise movement across the landscape. The importance from a genetic perspective of the more isolated North Island birds (1.6% of total population) needs to be further evaluated. From our results, we infer that the South Island black-billed gull management should focus on maintaining several populations within each region rather than focusing on single specific colonies or river catchments. Future study is needed to investigate the genetic structure of populations at the northern limit of the species' range, and identify the mechanisms behind, and extent of, the hybridisation between red-billed and black-billed gulls.

Genotyping-by-sequencing supports a genetic basis for wing reduction in an alpine New Zealand stonefly.

Wing polymorphism is a prominent feature of numerous insect groups, but the genomic basis for this diversity remains poorly understood. Wing reduction is a commonly observed trait in many species of stoneflies, particularly in cold or alpine environments. The widespread New Zealand stonefly Zelandoperla fenestrata species group (Z. fenestrata, Z. tillyardi, Z. pennulata) contains populations ranging from fully winged (macropterous) to vestigial-winged (micropterous), with the latter phenotype typically associated with high altitudes. The presence of flightless forms on numerous mountain ranges, separated by lowland fully winged populations, suggests wing reduction has occurred multiple times. We use Genotyping by Sequencing (GBS) to test for genetic differentiation between fully winged (n = 62) and vestigial-winged (n = 34) individuals, sampled from a sympatric population of distinct wing morphotypes, to test for a genetic basis for wing morphology. While we found no population genetic differentiation between these two morphotypes across 6,843 SNP loci, we did detect several outlier loci that strongly differentiated morphotypes across independent tests. These findings indicate that small regions of the genome are likely to be highly differentiated between morphotypes, suggesting a genetic basis for wing reduction. Our results provide a clear basis for ongoing genomic analysis to elucidate critical regulatory pathways for wing development in Pterygota.

The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand.

The house mouse (Mus musculus) provides a fascinating system for studying both the genomic basis of reproductive isolation, and the patterns of human-mediated dispersal. New Zealand has a complex history of mouse invasions, and the living descendants of these invaders have genetic ancestry from all three subspecies, although most are primarily descended from M. m. domesticus. We used the GigaMUGA genotyping array (approximately 135 000 loci) to describe the genomic ancestry of 161 mice, sampled from 34 locations from across New Zealand (and one Australian city-Sydney). Of these, two populations, one in the south of the South Island, and one on Chatham Island, showed complete mitochondrial lineage capture, featuring two different lineages of M. m. castaneus mitochondrial DNA but with only M. m. domesticus nuclear ancestry detectable. Mice in the northern and southern parts of the North Island had small traces (approx. 2-3%) of M. m. castaneus nuclear ancestry, and mice in the upper South Island had approximately 7-8% M. m. musculus nuclear ancestry including some Y-chromosomal ancestry-though no detectable M. m. musculus mitochondrial ancestry. This is the most thorough genomic study of introduced populations of house mice yet conducted, and will have relevance to studies of the isolation mechanisms separating subspecies of mice.

Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka).

Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.

An ancient selective sweep linked to reproductive life history evolution in sockeye salmon.

Study of parallel (or convergent) phenotypic evolution can provide important insights into processes driving sympatric, ecologically-mediated divergence and speciation, as ecotype pairs may provide a biological replicate of the underlying signals and mechanisms. Here, we provide evidence for a selective sweep creating an island of divergence associated with reproductive behavior in sockeye salmon (Oncorhynchus nerka), identifying a series of linked single nucleotide polymorphisms across a ~22,733 basepair region spanning the leucine-rich repeat-containing protein 9 gene exhibiting signatures of divergent selection associated with stream- and shore-spawning in both anadromous and resident forms across their pan-Pacific distribution. This divergence likely occurred ~3.8 Mya (95% HPD = 2.1-6.03 Mya), after sockeye separated from pink (O. gorbuscha) and chum (O. keta) salmon, but prior to the Pleistocene glaciations. Our results suggest recurrent evolution of reproductive ecotypes across the native range of O. nerka is at least partially associated with divergent selection of pre-existing genetic variation within or linked to this region. As sockeye salmon are unique among Pacific salmonids in their flexibility to spawn in lake-shore benthic environments, this region provides great promise for continued investigation of the genomic basis of O. nerka life history evolution, and, more broadly, for increasing our understanding of the heritable basis of adaptation of complex traits in novel environments.

Sockeye salmon repatriation leads to population re-establishment and rapid introgression with native kokanee.

Re-establishing salmonid populations to areas historically occupied has the substantial potential for conservation gains; however, such interventions also risk negatively impacting native resident stocks. Here, we assessed the success of the hatchery-assisted reintroduction of anadromous sockeye salmon (Oncorhynchus nerka) into Skaha Lake, British Columbia, Canada, and evaluated the genetic consequences for native kokanee, a freshwater-obligate ecotype, using single nucleotide polymorphism genotypic data collected from the reference samples of spawning Okanagan River sockeye and Skaha Lake kokanee presockeye reintroduction, along with annual trawl survey and angler-caught samples obtained over an eight-year period. Significant differentiation was detected between sockeye and kokanee reference samples, with >99% stock assignment. Low proportions of sockeye and hybrids were detected within 2008 and 2010 age-0 trawl samples; however, by 2012, 28% were sockeye, rising to 41% in 2014. The number of hybrids detected rose proportionally with the increase in sockeye and exhibited an intermediate phenotype. Our results indicate that the reintroduction of anadromous sockeye to Skaha Lake is succeeding, with large numbers returning to spawn. However, hybridization with native kokanee is of concern due to the potential for demographic or genetic swamping, with ongoing genetic monitoring necessary to assess the long-term effects of introgression and to support interactive fisheries management.

A description of sleep behaviour in healthy late pregnancy, and the accuracy of self-reports.

BACKGROUND: The importance of maternal sleep and its contribution to maternal and fetal health during pregnancy is increasingly being recognised. However, the ability to accurately recall sleep practices during pregnancy has been questioned. The aim of this study is to test the accuracy of recall of normal sleep practices in late pregnancy. METHODS: Thirty healthy women between 35 and 38 weeks of gestation underwent level III respiratory polysomnography (PSG) with infrared digital video recordings in their own homes. Data regarding sleep positions, number of times getting out of bed during the night and respiratory measures were collected. A sleep questionnaire was administered the morning after the recorded sleep. Continuous data were assessed using Spearman's Rho and Bland-Altman. Cohen's Kappa was used to assess recall in the categorical variables. RESULTS: Two-thirds of participants went to sleep on their left side. There was good agreement in sleep onset position between video and questionnaire data (Kappa 0.52), however the there was poor agreement on position on wakening (Kappa 0.24). The number of times getting out of bed during the night was accurately recalled (Kappa 0.65). Twenty five out of 30 participants snored as recorded by PSG. Questionnaire data was inaccurate for this measure. Bland-Altman plots demonstrated acceptable agreement between video and questionnaire data for estimated sleep duration, but not the time taken to fall asleep (sleep latency). One participant had mild obstructive sleep apnoea and another probable high upper airways resistance. CONCLUSIONS: Sleep onset position, sleep duration and the number of times getting out of bed during the night were accurately recalled, but sleep latency and sleep position on waking were not. This study identifies the sleep variables that can be accurately obtained by questionnaire and those that cannot.

The complete mitochondrial genomes of two chiton species (Sypharochiton pelliserpentis and Sypharochiton sinclairi) obtained using Illumina next generation sequencing.

Using an Illumina platform, we shot-gun sequenced the complete mitochondrial genomes of two sister chiton species (Sypharochiton pelliserpentis and Sypharochiton sinclairi) to an average coverage of 172× and 60×, respectively. We performed a de novo assembly using SOAPdenovo2 and determined the total mitogenome lengths to be 15,048 and 15,028 bps, respectively. The gene organization was similar to that of other chitons, with 13 protein-coding genes, 24 transfer RNAs and 2 ribosomal RNAs. These data will contribute for resolving the taxonomy and population genetic structures of these species.

Genomics and the challenging translation into conservation practice.

The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.

Patent foramen ovale closure in the treatment of obstructive sleep apnea.

Obstructive sleep apnea (OSA) and patent foramen ovale (PFO) are common conditions and may coexist. In patients with OSA, increases in right-to-left shunting across a PFO may result in increased burden of hypoxia, although the effect of this is unknown. We report the cases of 3 patients with highly symptomatic OSA and PFO who underwent percutaneous closure with the Coherex FlatStent PFO Closure System. Although PFO closure can be achieved with minimally invasive techniques and low rates of adverse events, its importance in reducing hypoxia in this population is unknown. PFO closure may result in improvement in apneas and symptoms in selected OSA patients and may impact cardiovascular events in this group through hypoxia-mediated or other unrecognized mechanisms.

Effect of tubing condensate on non-invasive positive pressure ventilators tested under simulated clinical conditions.

RATIONALE: Water condensate in the humidifier tubing can affect bi-level ventilation by narrowing tube diameter and increasing airflow resistance. We investigated room temperature and tubing type as ways to reduce condensate and its effect on bi-level triggering and pressure delivery. In this bench study, the aim was to test the hypothesis that a relationship exists between room temperature and tubing condensate. METHODS: Using a patient simulator, a Res-med bi-level device was set to 18/8 cm H(2)O and run for 6 h at room temperatures of 16°C, 18°C and 20°C. The built-in humidifier was set to a low, medium or high setting while using unheated or insulated tubing or replaced with a humidifier using heated tubing. Humidifier output, condensate, mask pressure and triggering delay of the bi-level were measured at 1 and 6 h using an infrared hygrometer, metric weights, Honeywell pressure transducer and TSI pneumotach. RESULTS: When humidity output exceeded 17.5 mg H(2)O/L, inspiratory pressure fell by 2-15 cm H(2)O and triggering was delayed by 0.2-0.9 s. Heating the tubing avoided any such ventilatory effect whereas warmer room temperatures or insulating the tubing were of marginal benefit. CONCLUSIONS: Users of bi-level ventilators need to be aware of this problem and its solution. Bi-level humidifier tubing may need to be heated to ensure correct humidification, pressure delivery and triggering.

Delays in the assessment and management of primary lung cancers in South Auckland.

AIM: To determine the patient characteristics, referral patterns and delays in assessment and treatment of patients with primary lung cancer in South Auckland, New Zealand and compare with international standards. METHODS: Retrospective review of the clinical records of 80 patients referred to a secondary care respiratory service and diagnosed with primary lung cancer in 2004. RESULTS: Eighty-five percent of inpatient referrals and 48.5% of outpatient referrals were for advanced stage lung cancers. The median interval from receipt of outpatient referral to first chest physician assessment was 18 days, with median interval from the first chest physician assessment to bronchoscopy of 17 days and for staging CT chest of 16 days. For patients requiring a CT-guided percutaneous needle aspiration for diagnosis, there was a further median delay of 37 days after the initial CT scan. The median interval from the date of receipt of initial outpatient referral to diagnosis was 38 days, but for early stage lung cancers it was 54 days. The median interval to diagnosis for inpatient admissions was 6 days after the first respiratory assessment. CONCLUSION: The intervals for initial assessment, diagnosis and treatment of lung cancer in South Auckland do not meet the recommendations of international guidelines, especially for early stage lung cancers. Organisational and resource changes are required at each point in the diagnostic and management pathway to reduce delays.