Proposals on Kaplan–Meier plots in medical research and a survey of stakeholder views: KMunicate

OBJECTIVES: To examine reactions to the proposed improvements to standard Kaplan–Meier plots, the standard way to present time-to-event data, and to understand which (if any) facilitated better depiction of (1) the state of patients over time, and (2) uncertainty over time in the estimates of survival. DESIGN: A survey of stakeholders’ opinions on the proposals. SETTING: A web-based survey, open to international participation, for those with an interest in visualisation of time-to-event data. PARTICIPANTS: 1174 people participated in the survey over a 6-week period. Participation was global (although primarily Europe and North America) and represented a wide range of researchers (primarily statisticians and clinicians). MAIN OUTCOME MEASURES: Two outcome measures were of principal importance: (1) participants’ opinions of each proposal compared with a ‘standard’ Kaplan–Meier plot; and (2) participants’ overall ranking of the proposals (including the standard). RESULTS: Most proposals were more popular than the standard Kaplan–Meier plot. The most popular proposals in the two categories, respectively, were an extended table beneath the plot depicting the numbers at risk, censored and having experienced an event at periodic timepoints, and CIs around each Kaplan–Meier curve. CONCLUSION: This study produced a high response number, reflecting the importance of graphics for time-to-event data. Those producing and publishing Kaplan–Meier plots—both authors and journals—should, as a starting point, consider using the combination of the two favoured proposals

Spatial connectivity in mosquito-borne disease models: a systematic review of methods and assumptions

This is the final version. Available from The Royal Society via the DOI in this record.Data extracted from the studies included in this systematic review are available from https://github.com/sophie-a-lee/mbd_connectivity_review and archived in a permanent repository on Zenodo (http://doi.org/10.5281/zenodo.4706866).Spatial connectivity plays an important role in mosquito-borne disease transmission. Connectivity can arise for many reasons, including shared environments, vector ecology and human movement. This systematic review synthesizes the spatial methods used to model mosquito-borne diseases, their spatial connectivity assumptions and the data used to inform spatial model components. We identified 248 papers eligible for inclusion. Most used statistical models (84.2%), although mechanistic are increasingly used. We identified 17 spatial models which used one of four methods (spatial covariates, local regression, random effects/fields and movement matrices). Over 80% of studies assumed that connectivity was distance-based despite this approach ignoring distant connections and potentially oversimplifying the process of transmission. Studies were more likely to assume connectivity was driven by human movement if the disease was transmitted by an Aedes mosquito. Connectivity arising from human movement was more commonly assumed in studies using a mechanistic model, likely influenced by a lack of statistical models able to account for these connections. Although models have been increasing in complexity, it is important to select the most appropriate, parsimonious model available based on the research question, disease transmission process, the spatial scale and availability of data, and the way spatial connectivity is assumed to occur.Engineering and Physical Sciences Research Council (EPSRC)The Royal Societ

A taxonomy for vocal learning

Funding: ONR grant no. N00014-18-1-2062 and the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland). MASTS is funded by the Scottish Funding Council (grant no. HR09011) and contributing institutions.Humans and songbirds learn to sing or speak by listening to acoustic models, forming auditory templates, and then learning to produce vocalizations that match the templates. These taxa have evolved specialized telencephalic pathways to accomplish this complex form of vocal learning, which has been reported for very few other taxa. By contrast, the acoustic structure of most animal vocalizations is produced by species-specific vocal motor programmes in the brainstem that do not require auditory feedback. However, many mammals and birds can learn to fine-tune the acoustic features of inherited vocal motor patterns based upon listening to conspecifics or noise. These limited forms of vocal learning range from rapid alteration based on real-time auditory feedback to long-term changes of vocal repertoire and they may involve different mechanisms than complex vocal learning. Limited vocal learning can involve the brainstem, mid-brain and/or telencephalic networks. Understanding complex vocal learning, which underpins human speech, requires careful analysis of which species are capable of which forms of vocal learning. Selecting multiple animal models for comparing the neural pathways that generate these different forms of learning will provide a richer view of the evolution of complex vocal learning and the neural mechanisms that make it possible. This article is part of the theme issue 'What can animal communication teach us about human language?'Publisher PDFPeer reviewe

Cross-sectional study evaluating the impact of SARS-CoV-2 variants on Long COVID outcomes in UK hospital survivors

OBJECTIVES: COVID-19 studies report on hospital admission outcomes across SARS-CoV-2 waves of infection but knowledge of the impact of SARS-CoV-2 variants on the development of Long COVID in hospital survivors is limited. We sought to investigate Long COVID outcomes, aiming to compare outcomes in adult hospitalised survivors with known variants of concern during our first and second UK COVID-19 waves, prior to widespread vaccination. DESIGN: Prospective observational cross-sectional study. SETTING: Secondary care tertiary hospital in the UK. PARTICIPANTS: This study investigated Long COVID in 673 adults with laboratory-positive SARS-CoV-2 infection or clinically suspected COVID-19, 6 weeks after hospital discharge. We compared adults with wave 1 (wildtype variant, admitted from February to April 2020) and wave 2 patients (confirmed Alpha variant on viral sequencing (B.1.1.7), admitted from December 2020 to February 2021). OUTCOME MEASURES: Associations of Long COVID presence (one or more of 14 symptoms) and total number of Long COVID symptoms with SARS-CoV-2 variant were analysed using multiple logistic and Poisson regression, respectively. RESULTS: 322/400 (wave 1) and 248/273 (wave 2) patients completed follow-up. Predictors of increased total number of Long COVID symptoms included: pre-existing lung disease (adjusted count ratio (aCR)=1.26, 95% CI 1.07, 1.48) and more COVID-19 admission symptoms (aCR=1.07, 95% CI 1.02, 1.12). Weaker associations included increased length of inpatient stay (aCR=1.02, 95% CI 1.00, 1.03) and later review after discharge (aCR=1.00, 95% CI 1.00, 1.01). SARS-CoV-2 variant was not associated with Long COVID presence (OR=0.99, 95% CI 0.24, 4.20) or total number of symptoms (aCR=1.09, 95% CI 0.82, 1.44). CONCLUSIONS: Patients with chronic lung disease or greater COVID-19 admission symptoms have higher Long COVID risk. SARS-CoV-2 variant was not predictive of Long COVID though in wave 2 we identified fewer admission symptoms, improved clinical trajectory and outcomes. Addressing modifiable factors such as length of stay and timepoint of clinical review following discharge may enable clinicians to move from Long COVID risk stratification towards improving its outcome

Neural Correlates of Threat Perception: Neural Equivalence of Conspecific and Heterospecific Mobbing Calls Is Learned

Songbird auditory areas (i.e., CMM and NCM) are preferentially activated to playback of conspecific vocalizations relative to heterospecific and arbitrary noise [1]–[2]. Here, we asked if the neural response to auditory stimulation is not simply preferential for conspecific vocalizations but also for the information conveyed by the vocalization. Black-capped chickadees use their chick-a-dee mobbing call to recruit conspecifics and other avian species to mob perched predators [3]. Mobbing calls produced in response to smaller, higher-threat predators contain more “D” notes compared to those produced in response to larger, lower-threat predators and thus convey the degree of threat of predators [4]. We specifically asked whether the neural response varies with the degree of threat conveyed by the mobbing calls of chickadees and whether the neural response is the same for actual predator calls that correspond to the degree of threat of the chickadee mobbing calls. Our results demonstrate that, as degree of threat increases in conspecific chickadee mobbing calls, there is a corresponding increase in immediate early gene (IEG) expression in telencephalic auditory areas. We also demonstrate that as the degree of threat increases for the heterospecific predator, there is a corresponding increase in IEG expression in the auditory areas. Furthermore, there was no significant difference in the amount IEG expression between conspecific mobbing calls or heterospecific predator calls that were the same degree of threat. In a second experiment, using hand-reared chickadees without predator experience, we found more IEG expression in response to mobbing calls than corresponding predator calls, indicating that degree of threat is learned. Our results demonstrate that degree of threat corresponds to neural activity in the auditory areas and that threat can be conveyed by different species signals and that these signals must be learned

Impacts of climate change on plant diseases – opinions and trends

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases in the coming decades. This review addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods

A longitudinal study of environmental tobacco smoke exposure in children: Parental self reports versus age dependent biomarkers

<p>Abstract</p> <p>Background</p> <p>Awareness of the negative effects of smoking on children's health prompted a decrease in the self-reporting of parental tobacco use in periodic surveys from most industrialized countries. Our aim is to assess changes between ETS exposure at the end of pregnancy and at 4 years of age determined by the parents' self-report and measurement of cotinine in age related biological matrices.</p> <p>Methods</p> <p>The prospective birth cohort included 487 infants from Barcelona city (Spain). Mothers were asked about maternal and household smoking habit. Cord serum and children's urinary cotinine were analyzed in duplicate using a double antibody radioimmunoassay.</p> <p>Results</p> <p>At 4 years of age, the median urinary cotinine level in children increased 1.4 or 3.5 times when father or mother smoked, respectively. Cotinine levels in children's urine statistically differentiated children from smoking mothers (Geometric Mean (GM) 19.7 ng/ml; 95% CI 16.83–23.01) and exposed homes (GM 7.1 ng/ml; 95% CI 5.61–8.99) compared with non-exposed homes (GM 4.5 ng/ml; 95% CI 3.71–5.48). Maternal self-reported ETS exposure in homes declined in the four year span between the two time periods from 42.2% to 31.0% (p < 0.01). Nevertheless, most of the children considered non-exposed by their mothers had detectable levels of cotinine above 1 ng/mL in their urine.</p> <p>Conclusion</p> <p>We concluded that cotinine levels determined in cord blood and urine, respectively, were useful for categorizing the children exposed to smoking and showed that a certain increase in ETS exposure during the 4-year follow-up period occurred.</p

Smoke-free legislation and child health

In this paper, we aim to present an overview of the scientific literature on the link between smoke-free legislation and early-life health outcomes. Exposure to second-hand smoke is responsible for an estimated 166 ,000 child deaths each year worldwide. To protect people from tobacco smoke, the World Health Organization recommends the implementation of comprehensive smoke-free legislation that prohibits smoking in all public indoor spaces, including workplaces, bars and restaurants. The implementation of such legislation has been found to reduce tobacco smoke exposure, encourage people to quit smoking and improve adult health outcomes. There is an increasing body of evidence that shows that children also experience health benefits after implementation of smoke-free legislation. In addition to protecting children from tobacco smoke in public, the link between smoke-free legislation and improved child health is likely to be mediated via a decline in smoking during pregnancy and reduced exposure in the home environment. Recent studies have found that the implementation of smoke-free legislation is associated with a substantial decrease in the number of perinatal deaths, preterm births and hospital attendance for respiratory tract infections and asthma in children, although such benefits are not found in each study. With over 80% of the world’s population currently unprotected by comprehensive smoke-free laws, protecting (unborn) children from the adverse impact of tobacco smoking and SHS exposure holds great potential to benefit public health and should therefore be a key priority for policymakers and health workers alike