Big catch, little sharks: Insight into Peruvian small-scale longline fisheries.

PublishedJournal ArticleThis is the final version of the article. Available from Wiley Open Access via the DOI in this record.Shark take, driven by vast demand for meat and fins, is increasing. We set out to gain insights into the impact of small-scale longline fisheries in Peru. Onboard observers were used to document catch from 145 longline fishing trips (1668 fishing days) originating from Ilo, southern Peru. Fishing effort is divided into two seasons: targeting dolphinfish (Coryphaena hippurus; December to February) and sharks (March to November). A total of 16,610 sharks were observed caught, with 11,166 identified to species level. Of these, 70.6% were blue sharks (Prionace glauca), 28.4% short-fin mako sharks (Isurus oxyrinchus), and 1% were other species (including thresher (Alopias vulpinus), hammerhead (Sphyrna zygaena), porbeagle (Lamnus nasus), and other Carcharhinidae species (Carcharhinus brachyurus, Carcharhinus falciformis, Galeorhinus galeus). Mean ± SD catch per unit effort of 33.6 ± 10.9 sharks per 1000 hooks was calculated for the shark season and 1.9 ± 3.1 sharks per 1000 hooks were caught in the dolphinfish season. An average of 83.7% of sharks caught (74.7% blue sharks; 93.3% mako sharks) were deemed sexually immature and under the legal minimum landing size, which for species exhibiting k-selected life history traits can result in susceptibility to over exploitation. As these growing fisheries operate along the entire Peruvian coast and may catch millions of sharks per annum, we conclude that their continued expansion, along with ineffective legislative approaches resulting in removal of immature individuals, has the potential to threaten the sustainability of the fishery, its target species, and ecosystem. There is a need for additional monitoring and research to inform novel management strategies for sharks while maintaining fisher livelihoods.We would like to thank the members of the fishing communities who participated in this study, in particular the fishers who were willing to have an observer onboard. We acknowledge Pro Delphinus staff: Bernedo, Cuentas, Lopez, and Mamani, for their help in data collection. We are thankful also to Pro Delphinus staff Natalia Ortiz and Nadia Balducci for support in data entry. This study was conducted in conjunction with and funded by the Darwin Initiative Sustainable Artisanal Fisheries Initiative in Peru and an initial grant from the Oak Foundation through Duke University. MJW was funded by PRIMaRE. JAS and JCM received support from ORSAS and University of Exeter, respectively

Seasonal variation in daily patterns of social contacts in the European badger Meles meles

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Social interactions among hosts influence the persistence and spread of infectious pathogens. Daily 20 and seasonal variation in the frequency and type of social interactions will play an important role in 21 disease epidemiology, and alongside other factors may have an influence on wider disease dynamics 22 by causing seasonal forcing of infection, especially if the seasonal variation experienced by a 23 population is considerable. We explored temporal variation in within-group contacts in a high-24 density population of European badgers Meles meles naturally-infected with bovine tuberculosis. 25 Summer contacts were more likely and of longer duration during the daytime, while the frequency 26 and duration of winter contacts did not differ between day and night. In spring and autumn within-27 group contacts peaked at dawn and dusk, corresponding with when they were of shortest duration 28 with reduced potential for aerosol transmission of pathogens. Summer and winter could be critical 29 for bovine tuberculosis transmission in badgers, due to the high frequency and duration of contacts 30 during resting periods, and we discuss the links between this result and empirical data. This study 31 reveals clear seasonality in daily patterns of contact frequency and duration in species living in stable 32 social groups, suggesting that changes in social contacts could drive seasonal forcing of infection in 33 wildlife populations even when the number of individuals interacting remains similar.MJS is funded by NERC grant NE/M004546/1 awarded to RAM, DPC, DJH and MB, with RJD and the 386 APHA team at Woodchester Park, UK as project partners. Data were collected for NW’s PhD, funded 387 by Defra. We thank Jared Wilson-Aggarwal and two anonymous reviewers for useful comments and 388 Keith Silk for providing the photograph for Figure 1

The application of statistical network models in disease research

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Host social structure is fundamental to how infections spread and persist, and so the statistical modelling of static and dynamic social networks provides an invaluable tool to parameterise realistic epidemiological models. We present a practical guide to the application of network modelling frameworks for hypothesis testing related to social interactions and epidemiology, illustrating some approaches with worked examples using data from a population of wild European badgers Meles meles naturally infected with bovine tuberculosis. Different empirical network datasets generate particular statistical issues related to non-independence and sampling constraints. We therefore discuss the strengths and weaknesses of modelling approaches for different types of network data and for answering different questions relating to disease transmission. We argue that statistical modelling frameworks designed specifically for network analysis offer great potential in directly relating network structure to infection. They have the potential to be powerful tools in analysing empirical contact data used in epidemiological studies, but remain untested for use in networks of spatio-temporal associations. As a result, we argue that developments in the statistical analysis of empirical contact data are critical given the ready availability of dynamic network data from bio-logging studies. Furthermore, we encourage improved integration of statistical network approaches into epidemiological research to facilitate the generation of novel modelling frameworks and help extend our understanding of disease transmission in natural populations.M.J.S. is funded by a NERC standard grant (NE/M004546/1) awarded to R.A.M., D.P.C., D.J.H. and M.B., with the APHA team at Woodchester Park, UK (lead scientist is R.J.D.) as project partners

Long-time Low-latency Quantum Memory by Dynamical Decoupling

Quantum memory is a central component for quantum information processing devices, and will be required to provide high-fidelity storage of arbitrary states, long storage times and small access latencies. Despite growing interest in applying physical-layer error-suppression strategies to boost fidelities, it has not previously been possible to meet such competing demands with a single approach. Here we use an experimentally validated theoretical framework to identify periodic repetition of a high-order dynamical decoupling sequence as a systematic strategy to meet these challenges. We provide analytic bounds-validated by numerical calculations-on the characteristics of the relevant control sequences and show that a "stroboscopic saturation" of coherence, or coherence plateau, can be engineered, even in the presence of experimental imperfection. This permits high-fidelity storage for times that can be exceptionally long, meaning that our device-independent results should prove instrumental in producing practically useful quantum technologies.Comment: abstract and authors list fixe

Cost-effectiveness of stent-retriever thrombectomy in combination with IV t-PA compared with IV t-PA alone for acute ischemic stroke in the UK.

Objective: To evaluate the cost-effectiveness of neurothrombectomy with a stent retriever (Solitaire**Solitaire Revascularization Device is a registered trademark of Medtronic (Irvine, CA). View all notes Revascularization Device) in treating acute ischemic stroke patients from the UK healthcare provider perspective. Methods: A Markov model was developed to simulate health outcomes and costs of two therapies over a lifetime time horizon: stent-retriever thrombectomy in combination with intravenous tissue-type plasminogen activator (IV t-PA), and IV t-PA alone. The model incorporated an acute phase (0–90 days) and a rest of life phase (90+ days). Health states were defined by the modified Rankin Scale score. During the rest of life phase, patients remained in the same health state until a recurrent stroke or death. Clinical effectiveness and safety data were taken from the SWIFT PRIME study. Resource use and health state utilities were informed by published data. Results: Combined stent-retriever thrombectomy and IV t-PA led to improved quality-of-life and increased life expectancy compared to IV t-PA alone. The higher treatment costs associated with the use of stent-retriever thrombectomy were offset by long-term cost savings due to improved patient health status, leading to overall cost savings of £33 190 per patient and a net benefit of £79 402. Deterministic and probabilistic sensitivity analyses demonstrated that the results were robust to a wide range of parameter inputs. Limitations: The acute and long-term costs resource use data were taken from a study based on a patient population that was older and may have had additional comorbidities than the SWIFT PRIME population, resulting in costs that may not be representative of the cohort within this model. In addition, the estimates may not reflect stroke care today as no current evidence is available; however, the cost estimates were deemed reasonable by clinical opinion. Conclusions: Combined stent-retriever neurothrombectomy and IV t-PA is a cost-effective treatment for acute ischemic stroke compared with IV t-PA alone

Malaria mortality in Africa and Asia: evidence from INDEPTH health and demographic surveillance system sites.

BACKGROUND: Malaria continues to be a major cause of infectious disease mortality in tropical regions. However, deaths from malaria are most often not individually documented, and as a result overall understanding of malaria epidemiology is inadequate. INDEPTH Network members maintain population surveillance in Health and Demographic Surveillance System sites across Africa and Asia, in which individual deaths are followed up with verbal autopsies. OBJECTIVE: To present patterns of malaria mortality determined by verbal autopsy from INDEPTH sites across Africa and Asia, comparing these findings with other relevant information on malaria in the same regions. DESIGN: From a database covering 111,910 deaths over 12,204,043 person-years in 22 sites, in which verbal autopsy data were handled according to the WHO 2012 standard and processed using the InterVA-4 model, over 6,000 deaths were attributed to malaria. The overall period covered was 1992-2012, but two-thirds of the observations related to 2006-2012. These deaths were analysed by site, time period, age group and sex to investigate epidemiological differences in malaria mortality. RESULTS: Rates of malaria mortality varied by 1:10,000 across the sites, with generally low rates in Asia (one site recording no malaria deaths over 0.5 million person-years) and some of the highest rates in West Africa (Nouna, Burkina Faso: 2.47 per 1,000 person-years). Childhood malaria mortality rates were strongly correlated with Malaria Atlas Project estimates of Plasmodium falciparum parasite rates for the same locations. Adult malaria mortality rates, while lower than corresponding childhood rates, were strongly correlated with childhood rates at the site level. CONCLUSIONS: The wide variations observed in malaria mortality, which were nevertheless consistent with various other estimates, suggest that population-based registration of deaths using verbal autopsy is a useful approach to understanding the details of malaria epidemiology

Perils and pitfalls of mixed-effects regression models in biology

This is the final version. Available on open access from PeerJ via the DOI in this recordData Availability: The following information was supplied regarding data availability: The R code used to conduct all simulations in the paper is available in the Supplemental Files.Biological systems, at all scales of organisation from nucleic acids to ecosystems, are inherently complex and variable. Biologists therefore use statistical analyses to detect signal among this systemic noise. Statistical models infer trends, find functional relationships and detect differences that exist among groups or are caused by experimental manipulations. They also use statistical relationships to help predict uncertain futures. All branches of the biological sciences now embrace the possibilities of mixed-effects modelling and its flexible toolkit for partitioning noise and signal. The mixed-effects model is not, however, a panacea for poor experimental design, and should be used with caution when inferring or deducing the importance of both fixed and random effects. Here we describe a selection of the perils and pitfalls that are widespread in the biological literature, but can be avoided by careful reflection, modelling and model-checking. We focus on situations where incautious modelling risks exposure to these pitfalls and the drawing of incorrect conclusions. Our stance is that statements of significance, information content or credibility all have their place in biological research, as long as these statements are cautious and well-informed by checks on the validity of assumptions. Our intention is to reveal potential perils and pitfalls in mixed model estimation so that researchers can use these powerful approaches with greater awareness and confidence. Our examples are ecological, but translate easily to all branches of biology.University of Exete

Aquatic community response to volcanic eruptions on the Ecuadorian Andean flank: evidence from the palaeoecological record

Aquatic ecosystems in the tropical Andes are under increasing pressure from human modification of the landscape (deforestation and dams) and climatic change (increase of extreme events and 1.5 °C on average temperatures are projected for AD 2100). However, the resilience of these ecosystems to perturbations is poorly understood. Here we use a multi-proxy palaeoecological approach to assess the response of aquatic ecosystems to a major mechanism for natural disturbance, volcanic ash deposition. Specifically, we present data from two Neotropical lakes located on the eastern Andean flank of Ecuador. Laguna Pindo (1°27.132′S–78°04.847′W) is a tectonically formed closed basin surrounded by a dense mid-elevation forest, whereas Laguna Baños (0°19.328′S–78°09.175′W) is a glacially formed lake with an inflow and outflow in high Andean Páramo grasslands. In each lake we examined the dynamics of chironomids and other aquatic and semi-aquatic organisms to explore the effect of thick (> 5 cm) volcanic deposits on the aquatic communities in these two systems with different catchment features. In both lakes past volcanic ash deposition was evident from four large tephras dated to c.850 cal year BP (Pindo), and 4600, 3600 and 1500 cal year BP (Baños). Examination of the chironomid and aquatic assemblages before and after the ash depositions revealed no shift in composition at Pindo, but a major change at Baños occurred after the last event around 1500 cal year BP. Chironomids at Baños changed from an assemblage dominated by Pseudochironomus and Polypedilum nubifer-type to Cricotopus/Paratrichocladius type-II, and such a dominance lasted for approximately 380 years. We suggest that, despite potential changes in the water chemistry, the major effect on the chironomid community resulted from the thickness of the tephra being deposited, which acted to shallow the water body beyond a depth threshold. Changes in the aquatic flora and fauna at the base of the trophic chain can promote cascade effects that may deteriorate the ecosystem, especially when already influenced by human activities, such as deforestation and dams, which is frequent in the high Andes