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Understanding cellular metabolism is important across biotechnology and biomedical research and has critical implications in a broad range of normal and pathological conditions. Here, we introduce the user-friendly web-based platform ImmCellFie, which allows the comprehensive analysis of metabolic functions inferred from transcriptomic or proteomic data. We explain how to set up a run using publicly available omics data and how to visualize the results. The ImmCellFie algorithm pushes beyond conventional statistical enrichment and incorporates complex biological mechanisms to quantify cell activity. For complete details on the use and execution of this protocol, please refer to Richelle et al. (2021).1.

This paper discusses a method of determining the minimum safe altitude of an uncrewed aerial vehicle (UAV) at any point within a designated airspace by conducting a glide reachability analysis. Recently, fixed‐wing UAVs are more regularly deployed near population centers and in extreme environments, requiring increasingly robust emergency systems and planning. The long‐ranges and adverse terrain associated with monitoring the Volcán de Fuego in Guatemala by a team from the University of Bristol (UoB) increases the likelihood that motor failure would result in the aircraft being unable to Return To Home (RTH) and impossible to retrieve. A method for delineating a boundary representing the minimum safe altitude required for the aircraft to safely glide to the airfield in the event of a motor failure was developed within MATLAB, defined by the UAV's minimum glide angle in wind. This model was subsequently compared with flight data from UoB missions around Fuego to better improve its accuracy and analyze the limitations of the missions. [ABSTRACT FROM AUTHOR]

The concept of 'peopled landscapes' is based on the notion that it is not possible, nor socially or politically desirable, to remove people from the environment in the era of the Anthropocene. As such, it is necessary to document and develop ways to coexist and flourish.This review examines emergent scholarship about peopled landscapes and biodiversity conservation by considering invasive plant management and rewilding as social processes. While invasive plant management and rewilding are often understood as separate, thinking through social scientific research and examples from Australia and the UK, we demonstrate how both forms of human action in landscapes can be more usefully understood as social relations with nature involving social change and social action.Drawing attention to agency, practices and capacity, we show how diverse forms of human and nonhuman actions are recognised, attributed or acknowledged in biodiversity conservation in peopled landscapes.In practice, centring the idea of peopled landscapes (rather than conceiving of the environment as where the impact of people is minimised) shows how invasive plant management and rewilding can be understood as related responses to environmental problems.Flourishing and coexistence in peopled landscapes require recognition of the diverse human and nonhuman agencies that shape the politics of acceptable action, and illustrate the inseparability of environmental and social justice. Read the free Plain Language Summary for this article on the Journal blog. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

We know that networked infrastructures enable forms of mobility, energy use, and flows of data, and we know that modern life depends on these arrangements. We also know that relations between infrastructures and social practices are recursive, extensive, and multiple. But what of the detail? How do infrastructures shape the many practices to which they relate, and vice versa? The research we describe was designed to address these questions head on. We discuss the arrival and normalisation of gas central heating with reference to householders' experiences and practices and to the ambitions and decisions of utilities and city authorities. In the process, we identify forms of aggregation and of integration on which infrastructure – practice dynamics depend. In taking this approach, we demonstrate the relevance of practice theory for conceptualising and analysing 'large' social phenomena including transitions in energy systems and related patterns of demand. [ABSTRACT FROM AUTHOR]

Motivation As the number of public data resources continues to proliferate, identifying relevant datasets across heterogenous repositories is becoming critical to answering scientific questions. To help researchers navigate this data landscape, we developed Dug: a semantic search tool for biomedical datasets utilizing evidence-based relationships from curated knowledge graphs to find relevant datasets and explain why those results are returned. Results Developed through the National Heart, Lung and Blood Institute's (NHLBI) BioData Catalyst ecosystem, Dug has indexed more than 15 911 study variables from public datasets. On a manually curated search dataset, Dug's total recall (total relevant results/total results) of 0.79 outperformed default Elasticsearch's total recall of 0.76. When using synonyms or related concepts as search queries, Dug (0.36) far outperformed Elasticsearch (0.14) in terms of total recall with no significant loss in the precision of its top results. Availability and implementation Dug is freely available at https://github.com/helxplatform/dug. An example Dug deployment is also available for use at https://search.biodatacatalyst.renci.org/. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Commercial fisheries are increasingly interested in greater social acceptance of their operations and practices. For harvesters, achieving acceptance is complex because expectations arise from many societal groups who can differ greatly in their perceptions. Historically, third‐party certification programmes assisted industry in gaining market acceptance (from consumer and investor groups) by improving the ecological sustainability of fishing practices. This focus is diversifying as societal expectations expand beyond ecological concerns to encompass, for instance, equal access and fair distribution of benefits as well as fisheries management and ethical aspects. In this study, we draw on theoretical work from the social acceptance and social licence literature to create a conceptual model that includes eight variables, representing different aspects of societal approval of fisheries. We applied this model to examine the influence of third‐party certification on societal approval of fisheries in Western Australia (WA). Based on study respondents' perceptions, third‐party certification had a statistically significant influence on facilitating government and regulatory approval of industry. Most respondents perceived certification to facilitate industry acceptance from stakeholders, but this was less so for the local community and general public. Contrary to expectations, but perhaps specific to WA because seafood is mostly sold without the ecolabel, certification was less influential on domestic and export market acceptance. Our findings, in WA, highlight certification was not equally influential on all societal approval aspects. Additionally, the conceptual model is sufficiently flexible to assist other fisheries (and industries) in understanding the influence of certification (and other factors) on different societal approval aspects. [ABSTRACT FROM AUTHOR]

Alongside government driven management initiatives to achieve sustainable fisheries management, there remains a role for market-based mechanisms to improve fisheries outcomes. Market-based mechanisms are intended to create positive economic incentives that improve the status and management of fisheries. Research to understand consumer demand for certified fish is central but needs to be mirrored by supply side understanding including why fisheries decide to gain or retain certification and the impact of certification on them and other stakeholders involved. We apply semi-structured interviews in seven different Marine Stewardship Council (MSC) certified fisheries that operate in (or from) Western Australia with the aim of better understanding fisheries sector participation in certification schemes (the supply side) and the impacts and unintended benefits and costs of certification. We find that any positive economic impacts of certification were only realised in a limited number of MSC fisheries in Western Australia, which may be explained by the fact that only a small proportion of Western Australian state-managed fisheries are sold with the MSC label and ex-vessel or consumer market price premiums are therefore mostly not obtained. Positive impacts of certification in these Western Australian fisheries are more of a social and institutional nature, for example, greater social acceptability and increased efficiency in the governance process respectively. However, opinion is divided on whether the combined non-monetary and monetary benefits outweigh the costs. [ABSTRACT FROM AUTHOR]

The nexus of water–energy–food (WEF) is as apparent at the household scale as it is anywhere else. We introduce the "Nexus at Home" as a starting point for exploring the dynamics of WEF resource use and household sustainability. Drawing on two research projects we focus specifically on domestic kitchens as a site where practices of cooking, eating, cleaning and disposing of waste come together. While these practices have long been targets for policy intervention, existing approaches draw on a limited range of perspectives from the social sciences. Reflecting on our work with four non‐academic partners (Defra, BEIS, FSA, Waterwise), we consider how social practice and geographies of household sustainability research might be combined with the dictum of "nexus thinking" to re‐imagine the framing of policy and intervention to reduce the resource intensity of everyday life. Synthesising existing "home practices" literature in the context of the "live" policy problems raised by our partners, we seek to provide clear guidance for intervening in kitchen practices. We draw on one topic which has not yet been the subject of social practices research: fats, oils and grease (FOG) going down the kitchen plughole and contributing to widespread sewer blockages. In doing so we document the sequence of interrelated food provisioning activities through which WEF is put to use in domestic kitchens and contributes to FOG blockages in sewers. We reflect upon the multiple ways these practices are shaped by the rhythms of daily life, dynamics within the home, wider cultural conventions, and infrastructures. This paper contributes to the nascent transdisciplinary research agenda of translating home practices research into wider conceptualisations of "intervention," with a specific orientation towards academic and non‐academic stakeholders who are interested in influencing systems of sustainable consumption and production within, and across, the WEF sectors. [ABSTRACT FROM AUTHOR]

The modes of governing approach is developed to engage with governing structures and processes and recognize the plurality and multiplicity of governing sites and activities. This framework, applied to the practice of municipal waste management, illustrates the dynamic and multiple nature of governing.

This paper describes a series of proof‐of‐concept Beyond Visual Line Of Sight unmanned aerial vehicle flights which reached a range of up to 9 km and an altitude of 4,410 m Above Mean Sea Level over Volcán de Fuego in Guatemala, interacting with the volcanic plume on multiple occasions across a range of different conditions. Volcán de Fuego is an active volcano which emits gas and ash regularly, causing disruption to airlines operating from the international airport 50 km away and impacting the lives of the local population. Collection of data from within the plume develops scientists' understanding of the composition of the volcano's output and is of use to scientists, aviation, and hazard management groups alike. This paper presents preliminary results of multiple plume interceptions with multiple aircraft, carrying a variety of sensors. A plume‐detection metric is introduced, which uses a combination of flight data and atmospheric sensor data to identify flight through a volcanic plume. Future work will develop the automation of plume tracking such that reliable scientific data sets can be gathered in a robust manner. [ABSTRACT FROM AUTHOR]

Part 1 of this paper has discussed the uncertainties arising from gaps in knowledge or limited understanding of the processes involved in different natural hazard areas. Such deficits may include uncertainties about frequencies, process representations, parameters, present and future boundary conditions, consequences and impacts, and the meaning of observations in evaluating simulation models. These are the epistemic uncertainties that can be difficult to constrain, especially in terms of event or scenario probabilities, even as elicited probabilities rationalized on the basis of expert judgements. This paper reviews the issues raised by trying to quantify the effects of epistemic uncertainties. Such scientific uncertainties might have significant influence on decisions made, say, for risk management, so it is important to examine the sensitivity of such decisions to different feasible sets of assumptions, to communicate the meaning of associated uncertainty estimates, and to provide an audit trail for the analysis. A conceptual framework for good practice in dealing with epistemic uncertainties is outlined and the implications of applying the principles to natural hazard assessments are discussed. Six stages are recognized, with recommendations at each stage as follows: (1) framing the analysis, preferably with input from potential users; (2) evaluating the available data for epistemic uncertainties, especially when they might lead to inconsistencies; (3) eliciting information on sources of uncertainty from experts; (4) defining a workflow that will give reliable and accurate results; (5) assessing robustness to uncertainty, including the impact on any decisions that are dependent on the analysis; and (6) communicating the findings and meaning of the analysis to potential users, stakeholders, and decision makers. Visualizations are helpful in conveying the nature of the uncertainty outputs, while recognizing that the deeper epistemic uncertainties might not be readily amenable to visualizations. [ABSTRACT FROM AUTHOR]

This paper discusses how epistemic uncertainties are currently considered in the most widely occurring natural hazard areas, including floods, landslides and debris flows, dam safety, droughts, earthquakes, tsunamis, volcanic ash clouds and pyroclastic flows, and wind storms. Our aim is to provide an overview of the types of epistemic uncertainty in the analysis of these natural hazards and to discuss how they have been treated so far to bring out some commonalities and differences. The breadth of our study makes it difficult to go into great detail on each aspect covered here; hence the focus lies on providing an overview and on citing key literature. We find that in current probabilistic approaches to the problem, uncertainties are all too often treated as if, at some fundamental level, they are aleatory in nature. This can be a tempting choice when knowledge of more complex structures is difficult to determine but not acknowledging the epistemic nature of many sources of uncertainty will compromise any risk analysis. We do not imply that probabilistic uncertainty estimation necessarily ignores the epistemic nature of uncertainties in natural hazards; expert elicitation for example can be set within a probabilistic framework to do just that. However, we suggest that the use of simple aleatory distributional models, common in current practice, will underestimate the potential variability in assessing hazards, consequences, and risks. A commonality across all approaches is that every analysis is necessarily conditional on the assumptions made about the nature of the sources of epistemic uncertainty. It is therefore important to record the assumptions made and to evaluate their impact on the uncertainty estimate. Additional guidelines for good practice based on this review are suggested in the companion paper (Part 2). [ABSTRACT FROM AUTHOR]

This article argues that the emphasis on solving substantive “real-world” problems through interdisciplinary research collaboration can neglect the wider value created by such collaborations. Championing the role of a knowledge integration and reflection facilitator, the article contends that more recognition be given to the value of “spillover” effects associated with interdisciplinary modes of working, rather than focusing solely on knowledge outputs and impacts. Drawing on embedded research conducted in relation to a project on local energy futures involving physicists, architects and geographers, the paper illustrates such “spillover” in relation to academic practice in teaching, project management and research methods. Such “spillovers” signal that what travels in interdisciplinary working is much more than formal knowledge and point to potential long-term legacy effects from interdisciplinary working occurring back in the disciplines. [ABSTRACT FROM AUTHOR]

Thermal spray coatings have been used in many industries, and recently these coatings have found niche applications in new industries such as the semiconductor and electronics industry. Thermal spray coatings [...]

Part 1 of this paper has discussed the uncertainties arising from gaps in knowledge or limited understanding of the processes involved in different natural hazard areas. Such deficits may include uncertainties about frequencies, process representations, parameters, present and future boundary conditions, consequences and impacts, and the meaning of observations in evaluating simulation models. These are the epistemic uncertainties that can be difficult to constrain, especially in terms of event or scenario probabilities, even as elicited probabilities rationalised on the basis of expert judgements. This paper reviews the issues raised by trying to quantify the effects of epistemic uncertainties. Such scientific uncertainties might have significant influence on decisions made, say, for risk management, so it is important to examine the sensitivity of such decisions to different feasible sets of assumptions, to communicate the meaning of associated uncertainty estimates and to provide an audit trail for the analysis. A conceptual framework for good practice in dealing with epistemic uncertainties is outlined and implications of applying the principles to natural hazard science are discussed. [ABSTRACT FROM AUTHOR]

This paper discusses how epistemic uncertainties are considered in a number of different natural hazard areas including floods, landslides and debris flows, dam safety, droughts, earthquakes, tsunamis, volcanic ash clouds and pyroclastic flows, and wind storms. In each case it is common practice to treat most uncertainties in the form of aleatory probability distributions but this may lead to an underestimation of the resulting uncertainties in assessing the hazard, consequences and risk. It is suggested that such analyses might be usefully extended by looking at different scenarios of assumptions about sources of epistemic uncertainty, with a view to reducing the element of surprise in future hazard occurrences. Since every analysis is necessarily conditional on the assumptions made about the nature of sources of epistemic uncertainty it is also important to follow the guidelines for good practice suggested in the companion Part 2. [ABSTRACT FROM AUTHOR]

This transdisciplinary research case study sought to disrupt the usual ways public participation shapes future energy systems. An interdisciplinary group of academics and a self-assembling public of a North English town co-produced ‘bottom-up’ visions for a future local energy system by emphasizing local values, aspirations and desires around energy futures. The effects of participatory modelling are considered as part of a community visioning process on participants’ social learning and social capital. This paper examines both the within-process dynamics related to models and the impact of the outside process, political use of the models by the participants. Both a numerical model (to explore local electricity generation and demand) and a physical scale model of the town were developed to explore various aspects of participants’ visions. The case study shows that collaborative visioning of local energy systems can enhance social learning and social capital of communities. However, the effect of participatory modelling on these benefits is less clear. Tensions arise between ‘inspiring’ and ‘empowering’ role of visions. It is argued that the situatedness of the visioning processes needs to be recognized and integrated within broader aspects of governance and power relations. [ABSTRACT FROM AUTHOR]

BackgroundPredicting the risk of glycated hemoglobin (HbA1c) elevation can help identify patients with the potential for developing serious chronic health problems, such as diabetes. Early preventive interventions based upon advanced predictive models using electronic health records data for identifying such patients can ultimately help provide better health outcomes. ObjectiveOur study investigated the performance of predictive models to forecast HbA1c elevation levels by employing several machine learning models. We also examined the use of patient electronic health record longitudinal data in the performance of the predictive models. Explainable methods were employed to interpret the decisions made by the black box models. MethodsThis study employed multiple logistic regression, random forest, support vector machine, and logistic regression models, as well as a deep learning model (multilayer perceptron) to classify patients with normal (

Problems of climate change present new challenges for social theory. In this article we focus on the task of understanding and analyzing car dependence, using this as a case through which to introduce and explore what we take to be central but underdeveloped questions about how infrastructures and complexes of social practice connect across space and time. In taking this approach we work with the proposition that forms of energy consumption, including those associated with automobility, are usefully understood as outcomes of interconnected patterns of social practices, including working, shopping, visiting friends and family, going to school, and so forth. We also acknowledge that social practices are partly constituted by, and always embedded in material arrangements. Linking these two features together, we suggest that forms of car dependence emerge through the intersection of infrastructural arrangements that are integral to the conduct of many practices at once. We consequently explore the significance of professional – and not only ‘ordinary’ – practices, especially those of planners and designers who are involved in reconfiguring infrastructures of different scales, and in the practice dynamics that follow. [ABSTRACT FROM AUTHOR]

Provenance is fundamentally about foods' point of origin. It is thus, unsurprising that studies of food provenance typically focus on circumstances of production and the routes foods follow to get to situations of exchange and, to a lesser extent, final consumption. However, this dominant framing leads to an asymmetry of attention between production and consumption. By neglecting the situatedness of food purchase and use, much of what makes provenance meaningful and productive for consumers is missed. This paper draws upon qualitative and ethnographic data to explore why and how it sometimes matters where food comes from. What emerges is an expanded and problematized practical understanding of provenance, where concerns for the point of origin is generally inseparable from, and subsumed within, a broader range of ethical concerns about where food comes from. [ABSTRACT FROM AUTHOR]

Two significant realms of social anxiety, visible in the discourses of media and public policy, potentially pull practices of home food provisioning in conflicting directions. On the one hand, campaigns to reduce the astonishing levels of food waste generated in the UK moralize acts of both food saving (such as keeping and finding creative culinary uses for leftovers) and food disposal. On the other hand, agencies concerned with food safety, including food-poisoning, problematize common practices of thrift, saving and reuse around provisioning. The tensions that arise as these public discourses are negotiated together into domestic practices open up moments in which 'stuff' crosses the line from being food to being waste. This paper pursues this through the lens of qualitative and ethnographic data collected as part of a four-year European research programme concerned with consumer anxieties about food. Through focus groups, life-history interviews and observations, data emerged which give critical insights into processes from which food waste results. With a particular focus on how research participants negotiate use-by dates, we argue that interventions to reduce food waste can be enhanced by appreciating how food becomes waste through everyday practices. [ABSTRACT FROM AUTHOR]

Amidst growing concern about both nutrition and food safety, anxiety about a loss of everyday cooking skills is a common part of public discourse. Within both the media and academia, it is widely perceived that there has been an erosion of the skills held by previous generations with the development of convenience foods and kitchen technologies cited as culpable in 'deskilling' current and future generations. These discourses are paralleled in policy concerns, where the incidence of indigenous food-borne disease in the UK has led to the emergence of an understanding of consumer behaviour, within the food industry and among food scientists, based on assumptions about consumer 'ignorance' and poor food hygiene knowledge and cooking skills. These assumptions are accompanied by perceptions of a loss of 'common-sense' understandings about the spoilage and storage characteristics of food, supposedly characteristic of earlier generations. The complexity of cooking skills immediately invites closer attention to discourses of their assumed decline. This paper draws upon early findings from a current qualitative research project which focuses on patterns of continuity and change in families' domestic kitchen practices across three generations. Drawing mainly upon two family case studies, the data presented problematise assumptions that earlier generations were paragons of virtue in the context of both food hygiene and cooking. In taking a broader, life-course perspective, we highlight the absence of linearity in participants' engagement with cooking as they move between different transitional points throughout the life-course. [ABSTRACT FROM AUTHOR]

This descriptive study analyzes deficiency data disclosed in peer review reports of the AICPA's Center for Public Company Audit Firms Peer Review Program (CPCAF PRP). We analyze the reports of the largest 20 triennially inspected firms that have both a PCAOB inspection report and a CPCAF peer review report. The CPCAF focuses on audits of non-public companies, while the PCAOB focuses on public company audits. Our analysis identifies a number of interesting points. First, about 60 percent of the reports issued by the CPCAF and PCAOB identify at least one deficiency. Second, both CPCAF and PCAOB reports highlight the pervasiveness of insufficient documentation. Third, other common deficiencies in the CPCAF reports relate to incomplete or inaccurate management representation letters, incomplete financial statements and inaccurate audit reports, incomplete performance of analytical procedures, and insufficient review procedures. [ABSTRACT FROM AUTHOR]

Municipal waste management in the UK has undergone rapid transformation in recent years in pursuit of greater sustainability. In this paper we explore the environmental justice issues and tensions involved in this shift. After a brief overview of environmental justice debates and how they have been related to issues of waste management, we describe how the policies and processes underlying the transformation from an overwhelming dependence on landfill disposal towards more sustainable methods of management has been driven by European legislation embodying principles premised on fundamental environmental concerns of inter- and intra-generational equity. We analyse the key means through which these principles have been translated to restructure local authority practices and the environmental justice issues arising from the implementation of international policy in regional and local context. Finally, we reflect on the implications of this case study for implementation of policies intended to advance both sustainability and environmental justice. [ABSTRACT FROM AUTHOR]

Recent years have seen a rapid rise in the political saliency of the ever growing volumes of municipal waste produced in the UK. In this paper, we outline the preliminary findings of a research project that is examining the nature and development of municipal waste policy (MWP) in north-east England. We provide an overview of the changing national, regional and local policy framework for sustainable municipal waste policy, arguing that the European Landfill Directive has had a profound impact on policy priorities and goals at all levels. Nonetheless, commentators and policy makers alike have identified significant ‘barriers’ to progress, including institutional fragmentation, instability and uncertainty, financial constraints, and public participation. While the ‘barriers’ metaphor has served to identify some of the key challenges, we suggest that it offers only a partial view of the issues at hand and can serve to perpetuate an unhelpful division between the ‘technical’ and ‘social’, and between policy making and practice. In this paper, we develop a new conceptual framework for analysing MWP based on an understanding of the multiple modes of governing through which policy is constructed and contested. We argue that this approach is also relevant for other areas of environmental policy and planning which have, to date, only partially engaged with broader debates about the changing nature of the state and governance. Bringing these concerns into the analysis of environmental policy and planning is, we believe, a key challenge for future research. [ABSTRACT FROM AUTHOR]

A team from the University of Bristol have developed a method of operating fixed wing Unmanned Aerial Vehicles (UAVs) at long-range and high-altitude over Volcán de Fuego in Guatemala for the purposes of volcanic monitoring and ash-sampling. Conventionally, the mission plans must be carefully designed prior to flight, to cope with altitude gains in excess of 3000 m, reaching 9 km from the ground control station and 4500 m above mean sea level. This means the climb route cannot be modified mid-flight. At these scales, atmospheric conditions change over the course of a flight and so a real-time trajectory planner (RTTP) is desirable, calculating a route on-board the aircraft. This paper presents an RTTP based around a genetic algorithm optimisation running on a Raspberry Pi 3 B+, the first of its kind to be flown on-board a UAV. Four flights are presented, each having calculated a new and valid trajectory on-board, from the ground control station to the summit region of Volcań de Fuego. The RTTP flights are shown to have approximately equivalent efficiency characteristics to conventionally planned missions. This technology is promising for the future of long-range UAV operations and further development is likely to see significant energy and efficiency savings. [ABSTRACT FROM AUTHOR]