Ecologists need robust survey designs, sampling and analytical methods

1. Research that yields conflicting results rightly causes controversy. Where methodological weaknesses are apparent, there is ready opportunity for discord within the scientific community, which may undermine the entire study. 2. We use the debate about the role of dingoes Canis dingo in conservation in Australia as a case study for a phenomenon that is relevant to all applied ecologists, where conflicting results have been published in high quality journals and yet the problems with the methods used in these studies have led to significant controversy. 3. To alleviate such controversies, scientists need to use robust methods to ensure that their results are repeatable and defendable. To date, this has not occurred in Australia’s dingo debate due to the use of unvalidated indices that rely on unsupported assumptions. 4. We highlight the problems that poor methods have caused in this debate. We also reiterate our recommendations for practitioners, statisticians and researchers to work together to develop long-term, multi-site experimental research programmes using robust methods to understand the impacts of dingoes on mesopredators. 5. Synthesis & applications. Incorporating robust methods and appropriate experimental designs are needed to ensure that conservation actions are appropriately focused and are supported with robust results. Such actions will go a long way towards resolving the debate about the role of dingoes in conservation in Australia, and other, ecological debates

Do Lions Panthera leo Actively Select Prey or Do Prey Preferences Simply Reflect Chance Responses via Evolutionary Adaptations to Optimal Foraging?

Research on coursing predators has revealed that actions throughout the predatory behavioral sequence (using encounter rate, hunting rate, and kill rate as proxy measures of decisions) drive observed prey preferences. We tested whether similar actions drive the observed prey preferences of a stalking predator, the African lion Panthera leo. We conducted two 96 hour, continuous follows of lions in Addo Elephant National Park seasonally from December 2003 until November 2005 (16 follows), and compared prey encounter rate with prey abundance, hunt rate with prey encounter rate, and kill rate with prey hunt rate for the major prey species in Addo using Jacobs' electivity index. We found that lions encountered preferred prey species far more frequently than expected based on their abundance, and they hunted these species more frequently than expected based on this higher encounter rate. Lions responded variably to non-preferred and avoided prey species throughout the predatory sequence, although they hunted avoided prey far less frequently than expected based on the number of encounters of them. We conclude that actions of lions throughout the predatory behavioural sequence, but particularly early on, drive the prey preferences that have been documented for this species. Once a hunt is initiated, evolutionary adaptations to the predator-prey interactions drive hunting success

SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants

© 2018, The Author(s). Seagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php

Effects of seasonal and pandemic influenza on health-related quality of life, work and school absence in England: results from the Flu Watch cohort study

BACKGROUND: Estimates of health-related quality of life (HRQoL) and work/school absences for influenza are typically based on medically-attended cases or those meeting influenza-like-illness (ILI) case definitions, and thus biased towards severe disease. Although community influenza cases are more common, estimates of their effects on HRQoL and absences are limited. OBJECTIVES: To measure Quality-Adjusted Life Days and Years (QALDs and QALYs) lost and work/school absences among community cases of acute respiratory infections (ARI), ILI and influenza A and B and to estimate community burden of QALY loss and absences from influenza. PATIENTS/ METHODS: Flu Watch was a community cohort in England from 2006-2011. Participants were followed-up weekly. During respiratory illness they prospectively recorded daily symptoms, work/school absences and EQ-5D-3L data and submitted nasal swabs for RT-PCR influenza testing. RESULTS: Average QALD lost was 0.26, 0.93, 1.61 and 1.84 for ARI, ILI, H1N1pdm09 and influenza B cases respectively. 40% of influenza A cases and 24% of influenza B cases took time off work/school with an average duration of 3.6 days and 2.4 days respectively. In England, community influenza cases lost 24,300 QALYs in 2010/11 and had an estimated 2.9 million absences per season based on data from 2006/07 - 2009/10. CONCLUSIONS: Our QALDs and QALYs lost and work and school absence estimates are lower than previous estimates because we focus on community cases, most of which are mild, may not meet ILI definitions and do not result in healthcare consultations. Nevertheless, they contribute a substantial loss of HRQoL on a population level. This article is protected by copyright. All rights reserved

The dune effect on sand-transporting winds on Mars

Wind on Mars is a significant agent of contemporary surface change, yet the absence of in situ meteorological data hampers the understanding of surface–atmospheric interactions. Airflow models at length scales relevant to landform size now enable examination of conditions that might activate even small-scale bedforms (ripples) under certain contemporary wind regimes. Ripples have the potential to be used as modern ‘wind vanes’ on Mars. Here we use 3D airflow modelling to demonstrate that local dune topography exerts a strong influence on wind speed and direction and that ripple movement likely reflects steered wind direction for certain dune ridge shapes. The poor correlation of dune orientation with effective sand-transporting winds suggests that large dunes may not be mobile under modelled wind scenarios. This work highlights the need to first model winds at high resolution before inferring regional wind patterns from ripple movement or dune orientations on the surface of Mars today

Toward Chirality‐Encoded Domain Wall Logic

Nonvolatile logic networks based on spintronic and nanomagnetic technologies have the potential to create high‐speed, ultralow power computational architectures. This article explores the feasibility of “chirality‐encoded domain wall logic,” a nanomagnetic logic architecture where data are encoded by the chiral structures of mobile domain walls in networks of ferromagnetic nanowires and processed by the chiral structures' interactions with geometric features of the networks. High‐resolution magnetic imaging is used to test two critical functionalities: the inversion of domain wall chirality at tailored artificial defect sites (logical NOT gates) and the chirality‐selective output of domain walls from 2‐in‐1‐out nanowire junctions (common operation to AND/NAND/OR/NOR gates). The measurements demonstrate both operations can be performed to a good degree of fidelity even in the presence of complex magnetization dynamics that would normally be expected to destroy chirality‐encoded information. Together, these results represent a strong indication of the feasibility of devices where chiral magnetization textures are used to directly carry, rather than merely delineate, data

Management and control of tuberculosis control in socially complex groups: a research programme including three RCTs

Background: Socially complex groups, including people experiencing homelessness, prisoners and drug users, have very high levels of tuberculosis, often complicated by late diagnosis and difficulty in adhering to treatment. / Objective: To assess a series of interventions to improve tuberculosis control in socially complex groups. / Design: A series of observational surveys, evaluations and trials of interventions. / Setting: The pan-London Find&Treat service, which supports tuberculosis screening and case management in socially complex groups across London. / Participants: Socially complex groups with tuberculosis or at risk of tuberculosis, including people experiencing homelessness, prisoners, drug users and those at high risk of poor adherence to tuberculosis treatment. Interventions and main outcome measures We screened 491 people in homeless hostels and 511 people in prison for latent tuberculosis infection, human immunodeficiency virus, hepatitis B and hepatitis C. We evaluated an NHS-led prison radiographic screening programme. We conducted a cluster randomised controlled trial (2348 eligible people experiencing homelessness in 46 hostels) of the effectiveness of peer educators (22 hostels) compared with NHS staff (24 hostels) at encouraging the uptake of mobile radiographic screening. We initiated a trial of the use of point-of-care polymerase chain reaction diagnostics to rapidly confirm tuberculosis alongside mobile radiographic screening. We undertook a randomised controlled trial to improve treatment adherence, comparing face-to-face, directly observed treatment with video-observed treatment using a smartphone application. The primary outcome was completion of ≥ 80% of scheduled treatment observations over the first 2 months following enrolment. We assessed the cost-effectiveness of latent tuberculosis screening alongside radiographic screening of people experiencing homelessness. The costs of video-observed treatment and directly observed treatment were compared. / Results: In the homeless hostels, 16.5% of people experiencing homelessness had latent tuberculosis infection, 1.4% had current hepatitis B infection, 10.4% had hepatitis C infection and 1.0% had human immunodeficiency virus infection. When a quality-adjusted life-year is valued at £30,000, the latent tuberculosis screening of people experiencing homelessness was cost-effective provided treatment uptake was ≥ 25% (for a £20,000 quality-adjusted life-year threshold, treatment uptake would need to be > 50%). In prison, 12.6% of prisoners had latent tuberculosis infection, 1.9% had current hepatitis B infection, 4.2% had hepatitis C infection and 0.0% had human immunodeficiency virus infection. In both settings, levels of latent tuberculosis infection and blood-borne viruses were higher among injecting drug users. A total of 1484 prisoners were screened using chest radiography over a total of 112 screening days (new prisoner screening coverage was 43%). Twenty-nine radiographs were reported as potentially indicating tuberculosis. One prisoner began, and completed, antituberculosis treatment in prison. In the cluster randomised controlled trial of peer educators to increase screening uptake, the median uptake was 45% in the control arm and 40% in the intervention arm (adjusted risk ratio 0.98, 95% confidence interval 0.80 to 1.20). A rapid diagnostic service was established on the mobile radiographic unit but the trial of rapid diagnostics was abandoned because of recruitment and follow-up difficulties. We randomly assigned 112 patients to video-observed treatment and 114 patients to directly observed treatment. Fifty-eight per cent of those recruited had a history of homelessness, addiction, imprisonment or severe mental health problems. Seventy-eight (70%) of 112 patients on video-observed treatment achieved the primary outcome, compared with 35 (31%) of 114 patients on directly observed treatment (adjusted odds ratio 5.48, 95% confidence interval 3.10 to 9.68; p < 0.0001). Video-observed treatment was superior to directly observed treatment in all demographic and social risk factor subgroups. The cost for 6 months of treatment observation was £1645 for daily video-observed treatment, £3420 for directly observed treatment three times per week and £5700 for directly observed treatment five times per week. / Limitations: Recruitment was lower than anticipated for most of the studies. The peer advocate study may have been contaminated by the fact that the service was already using peer educators to support its work. / Conclusions: There are very high levels of latent tuberculosis infection among prisoners, people experiencing homelessness and drug users. Screening for latent infection in people experiencing homelessness alongside mobile radiographic screening would be cost-effective, providing the uptake of treatment was 25–50%. Despite ring-fenced funding, the NHS was unable to establish static radiographic screening programmes. Although we found no evidence that peer educators were more effective than health-care workers in encouraging the uptake of mobile radiographic screening, there may be wider benefits of including peer educators as part of the Find&Treat team. Utilising polymerase chain reaction-based rapid diagnostic testing on a mobile radiographic unit is feasible. Smartphone-enabled video-observed treatment is more effective and cheaper than directly observed treatment for ensuring that treatment is observed. / Future work: Trials of video-observed treatment in high-incidence settings are needed. / Trial registration: Current Controlled Trials ISRCTN17270334 and ISRCTN26184967. / Funding: This project was funded by the National Institute for Health Research (NIHR) Programme Grants for Applied Research programme and will be published in full in Programme Grants for Applied Research; Vol. 8, No. 9. See the NIHR Journals Library website for further project information

Bayesian reconstruction of SARS-CoV-2 transmissions highlights substantial proportion of negative serial intervals

BACKGROUND: The serial interval is a key epidemiological measure that quantifies the time between the onset of symptoms in an infector-infectee pair. It indicates how quickly new generations of cases appear, thus informing on the speed of an epidemic. Estimating the serial interval requires to identify pairs of infectors and infectees. Yet, most studies fail to assess the direction of transmission between cases and assume that the order of infections - and thus transmissions - strictly follows the order of symptom onsets, thereby imposing serial intervals to be positive. Because of the long and highly variable incubation period of SARS-CoV-2, this may not always be true (i.e an infectee may show symptoms before their infector) and negative serial intervals may occur. This study aims to estimate the serial interval of different SARS-CoV-2 variants whilst accounting for negative serial intervals. METHODS: This analysis included 5 842 symptomatic individuals with confirmed SARS-CoV-2 infection amongst 2 579 households from September 2020 to August 2022 across England & Wales. We used a Bayesian framework to infer who infected whom by exploring all transmission trees compatible with the observed dates of symptoms, based on a wide range of incubation period and generation time distributions compatible with estimates reported in the literature. Serial intervals were derived from the reconstructed transmission pairs, stratified by variants. RESULTS: We estimated that 22% (95% credible interval (CrI) 8-32%) of serial interval values are negative across all VOC. The mean serial interval was shortest for Omicron BA5 (2.02 days, 1.26-2.84) and longest for Alpha (3.37 days, 2.52-4.04). CONCLUSIONS: This study highlights the large proportion of negative serial intervals across SARS-CoV-2 variants. Because the serial interval is widely used to estimate transmissibility and forecast cases, these results may have critical implications for epidemic control

Reversibility of Frailty After Bridge-to-Transplant Ventricular Assist Device Implantation or Heart Transplantation.

BACKGROUND: We recently reported that frailty is independently predictive of increased mortality in patients with advanced heart failure referred for heart transplantation (HTx). The aim of this study was to assess the impact of frailty on short-term outcomes after bridge-to-transplant ventricular assist device (BTT-VAD) implantation and/or HTx and to determine if frailty is reversible after these procedures. METHODS: Between August 2013 and August 2016, 100 of 126 consecutive patients underwent frailty assessment using Fried's Frailty Phenotype before surgical intervention: 40 (21 nonfrail, 19 frail) BTT-VAD and 77 (60 nonfrail, 17 frail) HTx-including 17 of the 40 BTT-VAD supported patients. Postprocedural survival, intubation time, intensive care unit, and hospital length of stay were compared between frail and nonfrail groups. Twenty-six frail patients were reassessed at 2 months or longer postintervention. RESULTS: Frail patients had lower survival (63 ± 10% vs 94 ± 3% at 1 year, P = 0.012) and experienced significantly longer intensive care unit (11 vs 5 days, P = 0.002) and hospital (49 vs 25 days, P = 0.003) length of stay after surgical intervention compared with nonfrail patients. Twelve of 13 frail patients improved their frailty score after VAD (4.0 ± 0.8 to 1.4 ± 1.1, P < 0.001) and 12 of 13 frail patients improved their frailty score after HTx (3.2 ± 0.4 to 0.9 ± 0.9, P < 0.001). Handgrip strength and depression improved postintervention. Only a slight improvement in cognitive function was seen postintervention. CONCLUSIONS: Frail patients with advanced heart failure experience increased mortality and morbidity after surgical intervention with BTT-VAD or HTx. Among those who survive frailty is partly or completely reversible underscoring the importance of considering this factor as a dynamic not fixed entity

Spatio-temporal variation in predation by urban domestic cats (Felis catus) and the acceptability of possible management actions in the UK

Urban domestic cat (Felis catus) populations can attain exceedingly high densities and are not limited by natural prey availability. This has generated concerns that they may negatively affect prey populations, leading to calls for management. We enlisted cat-owners to record prey returned home to estimate patterns of predation by free-roaming pets in different localities within the town of Reading, UK and questionnaire surveys were used to quantify attitudes to different possible management strategies. Prey return rates were highly variable: only 20% of cats returned ≥4 dead prey annually. Consequently, approximately 65% of owners received no prey in a given season, but this declined to 22% after eight seasons. The estimated mean predation rate was 18.3 prey cat−1 year−1 but this varied markedly both spatially and temporally: per capita predation rates declined with increasing cat density. Comparisons with estimates of the density of six common bird prey species indicated that cats killed numbers equivalent to adult density on c. 39% of occasions. Population modeling studies suggest that such predation rates could significantly reduce the size of local bird populations for common urban species. Conversely, most urban residents did not consider cat predation to be a significant problem. Collar-mounted anti-predation devices were the only management action acceptable to the majority of urban residents (65%), but were less acceptable to cat-owners because of perceived risks to their pets; only 24% of cats were fitted with such devices. Overall, cat predation did appear to be of sufficient magnitude to affect some prey populations, although further investigation of some key aspects of cat predation is warranted. Management of the predation behavior of urban cat populations in the UK is likely to be challenging and achieving this would require considerable engagement with cat owners