Dev-ResNet: automated developmental event detection using deep learning.

Delineating developmental events is central to experimental research using early life stages, permitting widespread identification of changes in event timing between species and environments. Yet, identifying developmental events is incredibly challenging, limiting the scale, reproducibility and throughput of using early life stages in experimental biology. We introduce Dev-ResNet, a small and efficient 3D convolutional neural network capable of detecting developmental events characterised by both spatial and temporal features, such as the onset of cardiac function and radula activity. We demonstrate the efficacy of Dev-ResNet using 10 diverse functional events throughout the embryonic development of the great pond snail, Lymnaea stagnalis. Dev-ResNet was highly effective in detecting the onset of all events, including the identification of thermally induced decoupling of event timings. Dev-ResNet has broad applicability given the ubiquity of bioimaging in developmental biology, and the transferability of deep learning, and so we provide comprehensive scripts and documentation for applying Dev-ResNet to different biological systems.

The north-south divide? Macroalgal functional trait diversity and redundancy varies with intertidal aspect.

BACKGROUND AND AIMS: Marine macroalgae ('seaweeds') are critical to coastal ecosystem structure and function, but also vulnerable to the many environmental changes associated with anthropogenic climate change (ACC). The local habitat conditions underpinning observed and predicted ACC-driven changes in intertidal macroalgal communities are complex and probably site-specific and operate in addition to more commonly reported regional factors such as sea surface temperatures. METHODS: We examined how the composition and functional trait expression of macroalgal communities in SW England varied with aspect (i.e. north-south orientation) at four sites with opposing Equator- (EF) and Pole-facing (PF) surfaces. Previous work at these sites had established that average annual (low tide) temperatures vary by 1.6 °C and that EF-surfaces experience six-fold more frequent extremes (i.e. >30 °C). KEY RESULTS: PF macroalgal communities were consistently more taxon rich; 11 taxa were unique to PF habitats, with only one restricted to EF. Likewise, functional richness and dispersion were greater on PF-surfaces (dominated by algae with traits linked to rapid resource capture and utilization, but low desiccation tolerance), although differences in both taxon and functional richness were probably driven by the fact that less diverse EF-surfaces were dominated by desiccation-tolerant fucoids. CONCLUSIONS: Although we cannot disentangle the influence of temperature variation on algal ecophysiology from the indirect effects of aspect on species interactions (niche pre-emption, competition, grazing, etc.), our study system provides an excellent model for understanding how environmental variation at local scales affects community composition and functioning. By virtue of enhanced taxonomic diversity, PF-aspects supported higher functional diversity and, consequently, greater effective functional redundancy. These differences may imbue PF-aspects with resilience against environmental perturbation, but if predicted increases in global temperatures are realized, some PF-sites may shift to a depauperate, desiccation-tolerant seaweed community with a concomitant loss of functional diversity and redundancy.

Medical ethics education as translational bioethics.

We suggest that in the particular context of medical education, ethics can be considered in a similar way to other kinds of knowledge that are categorised and shaped by academics in the context of wider society. Moreover, the study of medical ethics education is translational in a manner loosely analogous to the study of medical education as adjunct to translational medicine. Some have suggested there is merit in the idea that much as translational research attempts to connect the laboratory scientist's work to its implications for patient care, translational ethics focuses on bringing ethics scholarship into the sphere of personal and public action. We distinguish the term 'translational ethics' (the study of ethics being translated between academy, classroom and clinic) from other prominent definitions in the bioethics literature. To do this, we build off a notion of knowledge translation that focuses on the nonlinear movement of information that comes to professionals through multiple competing sources. We suggest that this knowledge, and particularly knowledge about ethics, becomes embodied by the individual. It is through a reflective practice that internally embedded ethics knowledge might be modified, and this work might be best carried out with a moral community that maintains a sense of practical wisdom. Applying this translational approach to the study of medical ethics education can be both academically relevant and practically useful. This view of translation can help bridge the evident, multidirectional relationships between research, education and performance. It might also create further opportunities to develop medical ethics education theory.

Professional identity and GP trainers as educational leaders.

GP training in the UK has a long history of success, however that is measured. That success is in part due to the formality and credentialling that underlies preparation to take on that role of a GP teacher, which is somewhat under current threat due to workforce pressures. We identify three important factors associated with the GP trainer function [leadership, professional identity and clinical care improvement] that are not often analysed but are at some risk if preparation for the GP trainer role is reduced or devalued. Of particular note are the differing ways that GPs conceptualise their professional roles as teachers and clinicians, despite the transferable skills between them, the demonstrably improved patient care that occurs in practices that teach, and the necessary connections between educational theory and practice. We suggest that these areas define a research agenda ripe for exploration.

A phenomics approach reveals interspecific differences in integrated developmental responses to chronic elevated temperatures.

Phenomics, high-dimensional organismal phenotyping, is advanced as a solution to quantifying complex developmental responses to elevated temperatures. 'Energy proxy traits' (EPTs) measure the phenotype as a spectrum of energy values across different temporal frequencies from pixel value fluctuations of video. Although they have proven effective in measuring the biology of complex and dynamic developing organisms, their utility in assessing environmental sensitivity of different species is untested. Using EPTs, we assess the relative thermal sensitivities of embryos of three species of freshwater snail with marked differences in their developmental event timings. Embryos of Lymnaea stagnalis, Radix balthica and Physella acuta were videoed hourly for the duration of their embryonic development at two temperatures: 20°C and 25°C. The video was used to calculate EPTs for the duration of their embryonic development, and during discrete physiological windows in development. Changes in energy spectra during development identified marked differences in thermal sensitivities between species, and suggest a relatively heightened sensitivity of gross rates of embryonic physiology and behaviour in embryos of R. balthica, developmental-window-specific thermal responses that reflect ontogenetic differences in observable physiologies, and temperature-induced changes in physiological event timing. EPTs enabled comparison of high-dimensional spectral phenotypes, providing a unique capability for assessing sensitivity continuously in developing individuals. Such integrative and scalable phenotyping is a prerequisite for improved understanding of the sensitivity of early life stages of different species.

HeartCV: a tool for transferrable, automated measurement of heart rate and heart rate variability in transparent animals.

Heart function is a key component of whole-organismal physiology. Bioimaging is commonly, but not exclusively, used for quantifying heart function in transparent individuals, including early developmental stages of aquatic animals, many of which are transparent. However, a central limitation of many imaging-related methods is the lack of transferability between species, life-history stages and experimental approaches. Furthermore, locating the heart in mobile individuals remains challenging. Here, we present HeartCV: an open-source Python package for automated measurement of heart rate and heart rate variability that integrates automated localization and is transferrable across a wide range of species. We demonstrate the efficacy of HeartCV by comparing its outputs with measurements made manually for a number of very different species with contrasting heart morphologies. Lastly, we demonstrate the applicability of the software to different experimental approaches and to different dataset types, such as those corresponding to longitudinal studies.

Spectral phenotyping of embryonic development reveals integrative thermodynamic responses.

BACKGROUND: Energy proxy traits (EPTs) are a novel approach to high dimensional organismal phenotyping that quantify the spectrum of energy levels within different temporal frequencies associated with mean pixel value fluctuations from video. They offer significant potential in addressing the phenotyping bottleneck in biology and are effective at identifying lethal endpoints and measuring specific functional traits, but the extent to which they might contribute additional understanding of the phenotype remains unknown. Consequently, here we test the biological significance of EPTs and their responses relative to fundamental thermodynamic principles. We achieve this using the entire embryonic development of Radix balthica, a freshwater pond snail, at different temperatures (20, 25 & 30 °C) and comparing responses against predictions from Arrhenius' equation (Q10 = 2). RESULTS: We find that EPTs are thermally sensitive and their spectra of frequency response enable effective high-dimensional treatment clustering throughout organismal development. Temperature-specific deviation in EPTs from thermodynamic predictions were evident and indicative of physiological mitigation, although they differed markedly in their responses from manual measures. The EPT spectrum was effective in capturing aspects of the phenotype predictive of biological outcomes, and suggest that EPTs themselves may reflect levels of energy turnover. CONCLUSIONS: Whole-organismal biology is incredibly complex, and this contributes to the challenge of developing universal phenotyping approaches. Here, we demonstrate the biological relevance of a new holistic approach to phenotyping that is not constrained by preconceived notions of biological importance. Furthermore, we find that EPTs are an effective approach to measuring even the most dynamic life history stages.

A high-throughput and open-source platform for embryo phenomics.

Phenomics has the potential to facilitate significant advances in biology but requires the development of high-throughput technologies capable of generating and analysing high-dimensional data. There are significant challenges associated with building such technologies, not least those required for investigating dynamic processes such as embryonic development, during which high rates of temporal, spatial, and functional change are inherently difficult to capture. Here, we present EmbryoPhenomics, an accessible high-throughput platform for phenomics in aquatic embryos comprising an Open-source Video Microscope (OpenVIM) that produces high-resolution videos of multiple embryos under tightly controlled environmental conditions. These videos are then analysed by the Python package Embryo Computer Vision (EmbryoCV), which extracts phenomic data for morphological, physiological, behavioural, and proxy traits during the process of embryonic development. We demonstrate the broad-scale applicability of EmbryoPhenomics in a series of experiments assessing chronic, acute, and multistressor responses to environmental change (temperature and salinity) in >30 million images of >600 embryos of two species with markedly different patterns of development-the pond snail Radix balthica and the marine amphipod Orchestia gammarellus. The challenge of phenomics is significant but so too are the rewards, and it is particularly relevant to the urgent task of assessing complex organismal responses to current rates of environmental change. EmbryoPhenomics can acquire and process data capturing functional, temporal, and spatial responses in the earliest, most dynamic life stages and is potentially game changing for those interested in studying development and phenomics more widely.

Do aquatic ectotherms perform better under hypoxia after warm acclimation?

Aquatic animals increasingly encounter environmental hypoxia due to climate-related warming and/or eutrophication. Although acute warming typically reduces performance under hypoxia, the ability of organisms to modulate hypoxic performance via thermal acclimation is less understood. Here, we review the literature and ask whether hypoxic performance of aquatic ectotherms improves following warm acclimation. Interpretation of thermal acclimation effects is limited by reliance on data from experiments that are not designed to directly test for beneficial or detrimental effects on hypoxic performance. Most studies have tested hypoxic responses exclusively at test temperatures matching organisms' acclimation temperatures, precluding the possibility of distinguishing between acclimation and acute thermal effects. Only a few studies have applied appropriate methodology to identify beneficial thermal acclimation effects on hypoxic performance, i.e. acclimation to different temperatures prior to determining hypoxic responses at standardised test temperatures. These studies reveal that acute warming predominantly impairs hypoxic performance, whereas warm acclimation tends to be either beneficial or have no effect. If this generalises, we predict that warm-acclimated individuals in some species should outperform non-acclimated individuals under hypoxia. However, acclimation seems to only partially offset acute warming effects; therefore, aquatic ectotherms will probably display overall reduced hypoxic performance in the long term. Drawing on the appropriate methodology, future studies can quantify the ability of organisms to modulate hypoxic performance via (reversible) thermal acclimation and unravel the underlying mechanisms. Testing whether developmental acclimation and multigenerational effects allow for a more complete compensation is essential to allow us to predict species' resilience to chronically warmer, hypoxic environments.

Moral flux in primary care : the effect of complexity.

In this article, we examine the inter-relationship between moral theory and the unpredictable and complex world of primary health care, where the values of patient and doctor, or groups of patients and doctors, may often clash. We introduce complexity science and its relevance to primary care; going on to explore how it can assist in understanding ethical decision making, as well as considering implications for clinical practice. Throughout the article, we showcase aspects and key concepts using examples and a case study developed from our day-to-day experience working as clinical practitioners in primary care.

Universal metabolic constraints shape the evolutionary ecology of diving in animals.

Diving as a lifestyle has evolved on multiple occasions when air-breathing terrestrial animals invaded the aquatic realm, and diving performance shapes the ecology and behaviour of all air-breathing aquatic taxa, from small insects to great whales. Using the largest dataset yet assembled, we show that maximum dive duration increases predictably with body mass in both ectotherms and endotherms. Compared to endotherms, ectotherms can remain submerged for longer, but the mass scaling relationship for dive duration is much steeper in endotherms than in ectotherms. These differences in diving allometry can be fully explained by inherent differences between the two groups in their metabolic rate and how metabolism scales with body mass and temperature. Therefore, we suggest that similar constraints on oxygen storage and usage have shaped the evolutionary ecology of diving in all air-breathing animals, irrespective of their evolutionary history and metabolic mode. The steeper scaling relationship between body mass and dive duration in endotherms not only helps explain why the largest extant vertebrate divers are endothermic rather than ectothermic, but also fits well with the emerging consensus that large extinct tetrapod divers (e.g. plesiosaurs, ichthyosaurs and mosasaurs) were endothermic.

Both maternal and embryonic exposure to mild hypoxia influence embryonic development of the intertidal gastropod Littorina littorea.

There is growing evidence that maternal exposure to environmental stressors can alter offspring phenotype and increase fitness. Here, we investigate the relative and combined effects of maternal and developmental exposure to mild hypoxia (65 and 74% air saturation, respectively) on the growth and development of embryos of the marine gastropod Littorina littorea Differences in embryo morphological traits were driven by the developmental environment, whereas the maternal environment and interactive effects of maternal and developmental environment were the main driver of differences in the timing of developmental events. While developmental exposure to mild hypoxia significantly increased the area of an important respiratory organ, the velum, it significantly delayed hatching of veliger larvae and reduced their size at hatching and overall survival. Maternal exposure had a significant effect on these traits, and interacted with developmental exposure to influence the time of appearance of morphological characters, suggesting that both are important in affecting developmental trajectories. A comparison between embryos that successfully hatched and those that died in mild hypoxia revealed that survivors exhibited hypertrophy in the velum and associated pre-oral cilia, suggesting that these traits are linked with survival in low-oxygen environments. We conclude that both maternal and developmental environments shape offspring phenotype in a species with a complex developmental life history, and that plasticity in embryo morphology arising from exposure to even small reductions in oxygen tensions affects the hatching success of these embryos.

The effects of elevated temperature and PCO2 on the energetics and haemolymph pH homeostasis of juveniles of the European lobster, Homarus gammarus.

Regulation of extracellular acid-base balance, while maintaining energy metabolism, is recognised as an important aspect when defining an organism's sensitivity to environmental changes. This study investigated the haemolymph buffering capacity and energy metabolism (oxygen consumption, haemolymph [l-lactate] and [protein]) in early benthic juveniles (carapace length <40 mm) of the European lobster, Homarus gammarus, exposed to elevated temperature and PCO2 At 13°C, H. gammarus juveniles were able to fully compensate for acid-base disturbances caused by the exposure to elevated seawater PCO2  at levels associated with ocean acidification and carbon dioxide capture and storage (CCS) leakage scenarios, via haemolymph [HCO3-] regulation. However, metabolic rate remained constant and food consumption decreased under elevated PCO2 , indicating reduced energy availability. Juveniles at 17°C showed no ability to actively compensate haemolymph pH, resulting in decreased haemolymph pH particularly under CCS conditions. Early benthic juvenile lobsters at 17°C were not able to increase energy intake to offset increased energy demand and therefore appear to be unable to respond to acid-base disturbances due to increased PCO2 at elevated temperature. Analysis of haemolymph metabolites suggests that, even under control conditions, juveniles were energetically limited. They exhibited high haemolymph [l-lactate], indicating recourse to anaerobic metabolism. Low haemolymph [protein] was linked to minimal non-bicarbonate buffering and reduced oxygen transport capacity. We discuss these results in the context of potential impacts of ongoing ocean change and CCS leakage scenarios on the development of juvenile H. gammarus and future lobster populations and stocks.

Teaching and learning at the primary - secondary care interface: work in progress?

Teaching and learning across the primary -secondary care interface is more described than actually carried out. As such it could be said this mirrors patient care across the same interface. We argue that for very good reasons generalists and specialists could do a lot more learning together than they currently do. If they did this, patient care, particularly integrated care, would be significantly advanced. We describe some examples of how it can be done well and suggest ways in which such learning might be more generally achieved. We suggest not only that those who learn together work better together, but also that they innovate health care more.

Understanding the relationship between GP training and improved patient care - a qualitative study of GP educators.

INTRODUCTION: Previous research has highlighted the benefits of receiving care in a postgraduate GP training practice including improved patient satisfaction, more appropriate secondary care usage, cancer diagnosis, and antibiotic prescribing. Whilst the influence of being registered in a postgraduate GP training practice on patient outcomes is modest relative to other factors such as deprivation, disease burden, demography, and ethnicity, the reasons for this benefit is not clear. AIM: This study explores how GP trainers perceive engagement with clinical education influences patient care. METHODS: Socio-cultural theories were used as a framework for guiding the research. Semi-structured interviews were conducted with 11 GP educators. Interviews were recorded and transcribed verbatim. Data analysis involved thematic analysis. RESULTS: GP educators identified four overarching themes that, for them, seemed to explain how clinical education mediates its influence on patient care. These included: influencing through (i) educational leadership; (ii) learners; (iii) the educational process; and (iv) educational standards. DISCUSSION: Findings suggest that GP trainees have a significant effect on the learning environment, professional development of GP trainers, and patient care. The nature of the relationship between GP trainers and trainees appears far more bilateral than acknowledged in the apprenticeship model.

Does sex really matter? Explaining intraspecies variation in ocean acidification responses.

Ocean acidification (OA) poses a major threat to marine ecosystems globally, having significant ecological and economic importance. The number and complexity of experiments examining the effects of OA has substantially increased over the past decade, in an attempt to address multi-stressor interactions and long-term responses in an increasing range of aquatic organisms. However, differences in the response of males and females to elevated pCO2 have been investigated in fewer than 4% of studies to date, often being precluded by the difficulty of determining sex non-destructively, particularly in early life stages. Here we highlight that sex can significantly impact organism responses to OA, differentially affecting physiology, reproduction, biochemistry and ultimately survival. What is more, these impacts do not always conform to ecological theory based on differential resource allocation towards reproduction, which would predict females to be more sensitive to OA owing to the higher production cost of eggs compared with sperm. Therefore, non-sex-specific studies may overlook subtle but ecologically significant differences in the responses of males and females to OA, with consequences for forecasting the fate of natural populations in a near-future ocean.

Learning Together; part 2: training costs and health gain - a cost analysis.

Learning Together is a complex educational intervention aimed at improving health outcomes for children and young people. There is an additional cost as two doctors are seeing patients together for a longer appointment than a standard general practice (GP) appointment. Our approach combines the impact of the training clinics on activity in South London in 2014-15 with health gain, using NICE guidance and standards to allow comparison of training options. METHODS: Activity data was collected from Training Practices hosting Learning Together. A computer based model was developed to analyse the costs of the Learning Together intervention compared to usual training in a partial economic evaluation. The results of the model were used to value the health gain required to make the intervention cost effective. RESULTS: Data were returned for 363 patients booked into 61 clinics across 16 Training Practices. Learning Together clinics resulted in an increase in costs of £37 per clinic. Threshold analysis illustrated one child with a common illness like constipation needs to be well for two weeks, in one Practice hosting four training clinics for the clinics to be considered cost effective. CONCLUSION: Learning Together is of minimal training cost. Our threshold analysis produced a rubric that can be used locally to test cost effectiveness at a Practice or Programme level.

Learning Together 1: an educational model for training GPs, paediatricians: initial findings.

Learning Together is primarily an educational intervention, where paediatric registrars [SpRs] and General Practice (GP) registrars [GPSTs] see children together in a primary care setting. Over a six month period in 2013/2014, 44 learning pairs were set up mainly in North East and Central London. Proof of concept for the model at scale was achieved. Reported learning demonstrated: clinical learning themes of new knowledge, skill and communication skills; and collaborative themes of ongoing collaboration, satisfaction with team working and change in attitudes. These themes were identified in both sets of trainees. The self-reported learning is backed up by the results of a retrospective notes review of four common conditions based on NICE guidelines; constipation, asthma, feverish illness and eczema (CAFE). Guidance adherence improved from 57% before the intervention in solo GP training consultations to 72% during the joint clinic intervention (p < 0.01). After the intervention when the GP registrars returned to normal consultations, guidance adherence was 77% compared to before the intervention (p < 0.01). In addition 99% of the parents, who handed in feedback forms or took part in interviews, reported a good experience of care, and 87% reported increased confidence to manage their children's health following the consultation. A second, linked article examines the cost utility of Learning Together in its South London extension.

Differences in the timing of cardio-respiratory development determine whether marine gastropod embryos survive or die in hypoxia.

Physiological plasticity of early developmental stages is a key way by which organisms can survive and adapt to environmental change. We investigated developmental plasticity of aspects of the cardio-respiratory physiology of encapsulated embryos of a marine gastropod, Littorina obtusata, surviving exposure to moderate hypoxia (PO2 =8 kPa) and compared the development of these survivors with that of individuals that died before hatching. Individuals surviving hypoxia exhibited a slower rate of development and altered ontogeny of cardio-respiratory structure and function compared with normoxic controls (PO2 >20 kPa). The onset and development of the larval and adult hearts were delayed in chronological time in hypoxia, but both organs appeared earlier in developmental time and cardiac activity rates were greater. The velum, a transient, 'larval' organ thought to play a role in gas exchange, was larger in hypoxia but developed more slowly (in chronological time), and velar cilia-driven, rotational activity was lower. Despite these effects of hypoxia, 38% of individuals survived to hatching. Compared with those embryos that died during development, these surviving embryos had advanced expression of adult structures, i.e. a significantly earlier occurrence and greater activity of their adult heart and larger shells. In contrast, embryos that died retained larval cardio-respiratory features (the velum and larval heart) for longer in chronological time. Surviving embryos came from eggs with significantly higher albumen provisioning than those that died, suggesting an energetic component for advanced development of adult traits.

Do hotter temperatures increase the incidence of self-harm hospitalisations?

A relationship between air temperature and the incidence of suicide has been established in a number of previous studies. Interestingly, the relationship between geographical variation in temperature and suicide incidence has generally been found to be negative, while the relationship between temporal variation in temperature and suicide incidence has generally been found to be positive. It is less clear, however, how temperature relates to the incidence of self-harm. This topic is of particular importance given the presence of ongoing global warming. This study investigated the relationship between temperature and the incidence of self-harm resulting in hospitalisation in New Zealand. Self-harm hospitalisations by date and district for 1993-2009 were obtained from the Ministry of Health. Meteorological data was obtained from NIWA. Generalised linear mixed models were used to estimate the effects of three different components of variation in temperature: geographical, seasonal and irregular. Irregular (random) daily variation in temperature had a modest positive relationship with the incidence of acts of self-harm resulting in hospitalisation, with about 0.7% extra incidents for every 1 °C increase in temperature. However, there was no strong evidence for a positive effect of either seasonal or geographical variation in temperature. We conclude that temperature does appear to bear some relation to the incidence of self-harm, with irregular daily variation in temperature having a positive effect. However, inconsistencies in the effects of different components of variation in temperature make it challenging to accurately predict how global warming will influence the incidence of self-harm.