Australia as a global sink for the genetic diversity of avian influenza A virus.

Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.

A surplus no more? Variation in krill availability impacts reproductive rates of Antarctic baleen whales.

The krill surplus hypothesis of unlimited prey resources available for Antarctic predators due to commercial whaling in the 20th century has remained largely untested since the 1970s. Rapid warming of the Western Antarctic Peninsula (WAP) over the past 50 years has resulted in decreased seasonal ice cover and a reduction of krill. The latter is being exacerbated by a commercial krill fishery in the region. Despite this, humpback whale populations have increased but may be at a threshold for growth based on these human-induced changes. Understanding how climate-mediated variation in prey availability influences humpback whale population dynamics is critical for focused management and conservation actions. Using an 8-year dataset (2013-2020), we show that inter-annual humpback whale pregnancy rates, as determined from skin-blubber biopsy samples (n = 616), are positively correlated with krill availability and fluctuations in ice cover in the previous year. Pregnancy rates showed significant inter-annual variability, between 29% and 86%. Our results indicate that krill availability is in fact limiting and affecting reproductive rates, in contrast to the krill surplus hypothesis. This suggests that this population of humpback whales may be at a threshold for population growth due to prey limitations. As a result, continued warming and increased fishing along the WAP, which continue to reduce krill stocks, will likely impact this humpback whale population and other krill predators in the region. Humpback whales are sentinel species of ecosystem health, and changes in pregnancy rates can provide quantifiable signals of the impact of environmental change at the population level. Our findings must be considered paramount in developing new and more restrictive conservation and management plans for the Antarctic marine ecosystem and minimizing the negative impacts of human activities in the region.

Dynamic body acceleration as a proxy to predict the cost of locomotion in bottlenose dolphins.

Estimates of the energetic costs of locomotion (COL) at different activity levels are necessary to answer fundamental eco-physiological questions and to understand the impacts of anthropogenic disturbance to marine mammals. We combined estimates of energetic costs derived from breath-by-breath respirometry with measurements of overall dynamic body acceleration (ODBA) from biologging tags to validate ODBA as a proxy for COL in trained common bottlenose dolphins (Tursiops truncatus). We measured resting metabolic rate (RMR); mean individual RMR was 0.71-1.42 times that of a similarly sized terrestrial mammal and agreed with past measurements that used breath-by-breath and flow-through respirometry. We also measured energy expenditure during submerged swim trials, at primarily moderate exercise levels. We subtracted RMR to obtain COL, and normalized COL by body size to incorporate individual swimming efficiencies. We found both mass-specific energy expenditure and mass-specific COL were linearly related with ODBA. Measurements of activity level and cost of transport (the energy required to move a given distance) improve understanding of the COL in marine mammals. The strength of the correlation between ODBA and COL varied among individuals, but the overall relationship can be used at a broad scale to estimate the energetic costs of disturbance and daily locomotion costs to build energy budgets, and investigate the costs of diving in free-ranging animals where bio-logging data are available. We propose that a similar approach could be applied to other cetacean species.

Regression and Random Forest Machine Learning Have Limited Performance in Predicting Bowel Preparation in Veteran Population.

BACKGROUND: Inadequate bowel preparation undermines the quality of colonoscopy, but patients likely to be affected are difficult to identify beforehand. AIMS: This study aimed to develop, validate, and compare prediction models for bowel preparation inadequacy using conventional logistic regression (LR) and random forest machine learning (RFML). METHODS: We created a retrospective cohort of patients who underwent outpatient colonoscopy at a single VA medical center between January 2012 and October 2015. Candidate predictor variables were chosen after a literature review. We extracted all available predictor variables from the electronic medical record, and bowel preparation from the endoscopy database. The data were split into 70% training and 30% validation sets. Multivariable LR and RFML were used to predict preparation inadequacy as a dichotomous outcome. RESULTS: The cohort included 6,885 Veterans, of whom 964 (14%) had inadequate preparation. Using LR, the area under the receiver operating characteristic curve (AUC) for the validation cohort was 0.66 (95% CI 0.62, 0.69) and the Brier score, in which a lower score indicates better performance, was 0.11. Using RFML, the AUC for the validation cohort was 0.61 (95% CI 0.58, 0.65) and the Brier score was 0.12. CONCLUSIONS: LR and RFML had similar performance in predicting bowel preparation, which was modest and likely insufficient for use in practice. Future research is needed to identify additional predictor variables and to test other machine learning algorithms. At present, endoscopy units should focus on universal strategies to enhance preparation adequacy.

Diffusion of an innovation: growth in video capsule endoscopy in the U.S. Medicare population from 2003 to 2019.

BACKGROUND: Video capsule endoscopy (VCE), approved by the U.S. Food and Drug Administration (FDA) in 2001, represented a disruptive technology that transformed evaluation of the small intestine. Adoption of this technology over time and current use within the U.S. clinical population has not been well described. METHODS: To assess the growth of capsule endoscopy within the U.S. Medicare provider population (absolute growth and on a population-adjusted basis), characterize the providers performing VCE, and describe potential regional differences in use. Medicare summary data from 2003 to 2019 were used to retrospectively analyze capsule endoscopy use in a multiple cross-sectional design. In addition, detailed provider summary files were used from 2012 to 2018 to characterize provider demographics. RESULTS: VCE use grew rapidly from 2003 to 2008 followed by a plateau from 2008 to 2019. There was significant variation in use of VCE between states, with up to 10-fold variation between states (14.6 to 156.1 per 100,000 enrollees in 2018). During this time, the adjusted VCE use on a population-adjusted basis declined, reflecting saturation of growth. CONCLUSIONS: Growth of VCE use over time follows an S-shaped diffusion of innovation curve demonstrating a successful diffusion of innovation within gastroenterology. The lack of additional growth since 2008 suggests that current levels of use are well matched to overall population need within the constraints of reimbursement. Future studies should examine whether this lack of growth has implications for access and healthcare inequities.

A National Survey of Adoption of the 2018 American Cancer Society Colorectal Cancer Screening Guideline in Primary Care.

Recent data have shown increasing incidence of colorectal cancer (CRC) among those younger than 50 years of age.1,2 In response, the American Cancer Society (ACS) introduced new guidelines in May 2018 that recommend initiation of CRC screening in average-risk adults at age 45, which is 5 years earlier than existing recommendations from the US Preventive Services Task Force and US Multi-Society Task Force on Colorectal Cancer.3-5 Most screening colonoscopies are ordered directly by primary care providers (PCPs) via "direct" or "open.

Illegal fisheries, environmental crime, and the conservation of marine resources.

The illegal harvest of marine species within exclusive economic zones can have a strong impact on the function of local ecosystems and livelihoods of coastal communities. The complexity of these problems is often overlooked in the development of solutions, leading to ineffective and sometimes harmful social and environmental outcomes. One-dimensional, oversimplified perspectives can lead to conservation prescriptions that exacerbate social stressors. This is particularly critical in the case of international illegal trade of endangered, high-value species, which generate a value chain in which artisanal fishers are the first operational and often the weakest link of an intricate web. We examined 2 illegal fisheries, totoaba (Totoaba macdonaldi) and sea cucumber (Isostichopus badionotus and Holothuria floridana), in Mexico. Although these are 2 separate and independent fisheries, important ecological (resource condition, fishery impacts at the ecosystem level) and social (governance, markets) similarities improve understanding of their complexity. Our findings are relevant globally and show the need for interdisciplinary decision-making groups, community engagement, and the development of demand reduction measures.

Pesquerías Ilegales, Crímenes Ambientales y la Conservación de los Recursos Marinos Resumen La cosecha ilegal de especies marinas dentro de las zonas económicas exclusivas puede tener un impacto serio sobre la función de los ecosistemas locales y el economia de las comunidades costeras. La complejidad de estos problemas generalmente se ignora durante el desarrollo de soluciones, lo que conlleva a resultados ambientales y sociales poco efectivos y algunas veces dañinos. Las perspectivas unidimensionales y sobresimplificadas pueden derivar en prescripciones de conservación que empeoran las condiciones sociales sociales. Lo anterior es particularmente crítico para el caso del mercado ilegal de especies en peligro y de alto valor, lo que genera una cadena de valores en la que los pescadores tradicionales son el primer eslabón operativo y con frecuencia el más débil de una red intrincada. Examinamos dos pesquerías ilegales, la de la totoaba (Totoaba macdonaldi) y la del pepino de mar (Isostichopus badionotus y Holothuria floridana), en México. Aunque estas dos pesquerías son diferentes e independientes, las importantes similitudes ecológicas (estado del recurso, impactos de la pesquería a nivel de ecosistema) y sociales (governancia, mercados) mejoran el conocimiento de su complejidad. Nuestros hallazgos son relevantes a escala global y muestran la necesidad de tener grupos interdisciplinarios para tomar decisiones, la participación de la comunidad y el desarrollo de medidas para reducir la demanda por el producto pesquero.

Exploring movement patterns and changing distributions of baleen whales in the western North Atlantic using a decade of passive acoustic data.

Six baleen whale species are found in the temperate western North Atlantic Ocean, with limited information existing on the distribution and movement patterns for most. There is mounting evidence of distributional shifts in many species, including marine mammals, likely because of climate-driven changes in ocean temperature and circulation. Previous acoustic studies examined the occurrence of minke (Balaenoptera acutorostrata) and North Atlantic right whales (NARW; Eubalaena glacialis). This study assesses the acoustic presence of humpback (Megaptera novaeangliae), sei (B. borealis), fin (B. physalus), and blue whales (B. musculus) over a decade, based on daily detections of their vocalizations. Data collected from 2004 to 2014 on 281 bottom-mounted recorders, totaling 35,033 days, were processed using automated detection software and screened for each species' presence. A published study on NARW acoustics revealed significant changes in occurrence patterns between the periods of 2004-2010 and 2011-2014; therefore, these same time periods were examined here. All four species were present from the Southeast United States to Greenland; humpback whales were also present in the Caribbean. All species occurred throughout all regions in the winter, suggesting that baleen whales are widely distributed during these months. Each of the species showed significant changes in acoustic occurrence after 2010. Similar to NARWs, sei whales had higher acoustic occurrence in mid-Atlantic regions after 2010. Fin, blue, and sei whales were more frequently detected in the northern latitudes of the study area after 2010. Despite this general northward shift, all four species were detected less on the Scotian Shelf area after 2010, matching documented shifts in prey availability in this region. A decade of acoustic observations have shown important distributional changes over the range of baleen whales, mirroring known climatic shifts and identifying new habitats that will require further protection from anthropogenic threats like fixed fishing gear, shipping, and noise pollution.

Extreme diving in mammals: first estimates of behavioural aerobic dive limits in Cuvier's beaked whales.

We analysed 3680 dives from 23 satellite-linked tags deployed on Cuvier's beaked whales to assess the relationship between long duration dives and inter-deep dive intervals and to estimate aerobic dive limit (ADL). The median duration of presumed foraging dives was 59 min and 5% of dives exceeded 77.7 min. We found no relationship between the longest 5% of dive durations and the following inter-deep dive interval nor any relationship with the ventilation period immediately prior to or following a long dive. We suggest that Cuvier's beaked whales have low metabolic rates, high oxygen storage capacities and a high acid-buffering capacity to deal with the by-products of both aerobic and anaerobic metabolism, which enables them to extend dive durations and exploit their bathypelagic foraging habitats.

Increased Cost With Use of Brand-Name Bowel Preparation by Patients With Medicare Part D From 2013 to 2015.

High-quality bowel preparation (prep) before colonoscopy is essential for the success of the procedure.1 Bowel preps should be safe, tolerable, efficacious, and allow for visualization of polyps 5 mm or larger.2 Full-volume (4 L) polyethylene glycol-3350 with electrolyte solution (PEG-ELS) has been considered a standard bowel prep regimen, with good safety and efficacy profiles, and is available as a generic.2.

Detection and Circulation of a Novel Rabbit Hemorrhagic Disease Virus in Australia.

The highly virulent rabbit hemorrhagic disease virus (RHDV) has been widely used in Australia and New Zealand since the mid-1990s to control wild rabbits, an invasive vertebrate pest in these countries. In January 2014, an exotic RHDV was detected in Australia, and 8 additional outbreaks were reported in both domestic and wild rabbits in the 15 months following its detection. Full-length genomic analysis revealed that this virus is a recombinant containing an RHDVa capsid gene and nonstructural genes most closely related to nonpathogenic rabbit caliciviruses. Nationwide monitoring efforts need to be expanded to assess if the increasing number of different RHDV variants circulating in the Australian environment will affect biological control of rabbits. At the same time, updated vaccines and vaccination protocols are urgently needed to protect pet and farmed rabbits from these novel rabbit caliciviruses.

Selective reactions to different killer whale call categories in two delphinid species.

The risk of predation is often invoked as an important factor influencing the evolution of social organization in cetaceans, but little direct information is available about how these aquatic mammals respond to predators or other perceived threats. We used controlled playback experiments to examine the behavioral responses of short-finned pilot whales (Globicephala macrorhynchus) off Cape Hatteras, NC, USA, and Risso's dolphins (Grampus griseus) off the coast of Southern California, USA, to the calls of a potential predator, mammal-eating killer whales. We transmitted calls of mammal-eating killer whales, conspecifics and baleen whales to 10 pilot whales and four Risso's dolphins equipped with multi-sensor archival acoustic recording tags (DTAGs). Only playbacks of killer whale calls resulted in significant changes in tagged animal heading. The strong responses observed in both species occurred only following exposure to a subset of killer whale calls, all of which contained multiple non-linear properties. This finding suggests that these structural features of killer whale calls convey information about predatory risk to pilot whales and Risso's dolphins. The observed responses differed between the two species; pilot whales approached the sound source while Risso's dolphins fled following playbacks. These divergent responses likely reflect differences in anti-predator response mediated by the social structure of the two species.

Who is Responsible for What Happens Before, During, and After Colonoscopy? Results of a National Survey of Primary Care Physicians.

BACKGROUND AND AIMS: Primary care providers (PCPs) play a critical role in colon cancer screening by initiating referrals to gastroenterologists for colonoscopy, but little is known about their role in pre-colonoscopy bowel preparation selection and pre-colonoscopy follow-up care. This study aimed to better understand coordination of care between PCPs and gastroenterologists as well as the current availability of "open-access" screening colonoscopy. METHODS: A multiple-choice survey was developed to assess PCPs' experiences with open-access colonoscopy, their involvement in the pre-colonoscopy process, and follow-up after colonoscopy. The survey was distributed electronically to a nationally representative sample of PCPs, via the American College of Physicians (ACP) Research Center's Internal Medicine Insider Research Panel. RESULTS: Of 442 PCPs invited to participate, 210 responded (response rate, 210/442, 48%), and 29 were ineligible (spent <25% of their time on clinical care or placed no referrals to colonoscopy), yielding 181 completed surveys. A total of 39% reported that open access was "rarely" or "never" available in their practice setting. The majority reported that pre-colonoscopy care was coordinated by gastroenterologists rather than PCPs. For example, 93% reported that gastroenterologists were responsible for bowel preparation selection in their practice setting. Post-colonoscopy, 54% of PCPs reported that they were responsible for ordering subsequent colonoscopies. CONCLUSIONS: PCPs frequently coordinate follow-up care postprocedure but play a relatively minor role in the pre-colonoscopy bowel preparation process. Open access availability for screening colonoscopy remains limited in this national sample of PCPs.

A Deeper Look at the Small Bowel: Training Pathways in Video Capsule Endoscopy and Device-Assisted Enteroscopy.

BACKGROUND: Although there are guidelines for video capsule endoscopy (VCE) and device-assisted enteroscopy (DAE), little is known about fellowship training in these technologies. AIMS: The aims were to better characterize current small bowel endoscopy training in 3-year GI fellowship programs and 4th-year advanced endoscopy programs in the U.S. METHODS: We developed an online multiple-choice survey to assess current GI fellowship program training in small bowel endoscopy. The survey was distributed via email to GI fellowship program directors in the U.S. RESULTS: Of the 168 program directors contacted, 59 responded (response rate = 35.1%). There was no statistically significant difference in the availability of VCE or DAE between respondents and non-respondents. VCE training was universally available in 3-year training programs, with 84.8% (50/59) requiring it for fellows. The majority of 3-year GI fellows graduated with independence in VCE: 83.1% (49/59) of programs reported "most" or "all" graduates were able to read independently. DAE techniques were available in 86.4% of training programs (51/59). Training in DAE was more limited and shared between 3-year and 4th-year programs: 12.1% (7/58) of 3-year programs required training in DAE and 22.9% (8/35) of 4th-year programs required training in DAE . CONCLUSIONS: Training in VCE is widely available in U.S. GI fellowship programs, although programs have different ways of incorporating this training into the curriculum and of measuring competency. While DAE technology was available in the majority of programs, training was less frequently available, and training is shared between 3-year fellowship programs and 4th-year advanced endoscopy programs .

Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots.

Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce--in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers--and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority.

Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia.

To resolve the evolutionary history of rabbit hemorrhagic disease virus (RHDV), we performed a genomic analysis of the viral stocks imported and released as a biocontrol measure in Australia, as well as a global phylogenetic analysis. Importantly, conflicts were identified between the sequences determined here and those previously published that may have affected evolutionary rate estimates. By removing likely erroneous sequences, we show that RHDV emerged only shortly before its initial description in China.

The Challenges of Analyzing Behavioral Response Study Data: An Overview of the MOCHA (Multi-study OCean Acoustics Human Effects Analysis) Project.

This paper describes the MOCHA project which aims to develop novel approaches for the analysis of data collected during Behavioral Response Studies (BRSs). BRSs are experiments aimed at directly quantifying the effects of controlled dosages of natural or anthropogenic stimuli (typically sound) on marine mammal behavior. These experiments typically result in low sample size, relative to variability, and so we are looking at a number of studies in combination to maximize the gain from each one. We describe a suite of analytical tools applied to BRS data on beaked whales, including a simulation study aimed at informing future experimental design.

Effects of duty-cycled passive acoustic recordings on detecting the presence of beaked whales in the northwest Atlantic.

This study investigated the effects of using duty-cycled passive acoustic recordings to monitor the daily presence of beaked whale species at three locations in the northwest Atlantic. Continuous acoustic records were subsampled to simulate duty cycles of 50%, 25%, and 10% and cycle period durations from 10 to 60 min. Short, frequent listening periods were most effective for assessing the daily presence of beaked whales. Furthermore, subsampling at low duty cycles led to consistently greater underestimation of Mesoplodon species than either Cuvier's beaked whales or northern bottlenose whales, leading to a potential bias in estimation of relative species occurrence.

Hendra Virus Infection in Dog, Australia, 2013.

Hendra virus occasionally causes severe disease in horses and humans. In Australia in 2013, infection was detected in a dog that had been in contact with an infected horse. Abnormalities and viral RNA were found in the dog's kidney, brain, lymph nodes, spleen, and liver. Dogs should be kept away from infected horses.