Nanopore sequencing of ocean microbiomes

Ocean microbiomes are responsible for the majority of global primary production, and are crucial for global biogeochemical cycles. Eukaryotic phytoplankton contribute to the carbon cycle which is important for the climate, with polar communities making a disproportionate contribution. These communities are threatened by climate change, and it is important to understand their distribution and interactions so that these impacts can be modelled and monitored. Ocean microbiomes have not been well characterised, but nanopore sequencing could be used to study them with long-reads and in situ sequencing. This project piloted the use of nanopore sequencing for studying ocean microbes to improve our understanding of their genomes, communities, and interactions. A genome assembly was produced for a haploid Emiliania huxleyi strain, to complement the single publicly available diploid genome assembly. The new assembly uses a hybrid approach and represents a significant improvement on the diploid assembly with contiguity and completeness comparable to other recent haptophyte genome assemblies. In situ nanopore sequencing and real-time taxonomic classification onboard the RRS Discovery in the Southern Ocean established the utility of nanopore sequencing on polar ocean research cruises, and provided insights into polar ocean microbiomes. Additional samples were collected for land-based sequencing which identified key communities such as diatoms, and produced assembly-free functional annotations. An improved protocol was developed to reduce sampling requirements, and reliance on toxic reagents, for potential use by citizen scientists. The improved protocol was successfully implemented in an in situ sequencing experiment with real-time analysis on the Norfolk coast, and a time-course analysis to investigate population flux. These experiments showed the benefits of nanopore sequencing for researchers studying ocean microbiomes, and provided insights into their genomes, and communities. With constant improvements to the technology, nanopore sequencing will only become more useful for the study of ocean microbial communities

Diatoms and their microbiomes in complex and changing polar oceans

Diatoms, a key group of polar marine microbes, support highly productive ocean ecosystems. Like all life on earth, diatoms do not live in isolation, and they are therefore under constant biotic and abiotic pressures which directly influence their evolution through natural selection. Despite their importance in polar ecosystems, polar diatoms are understudied compared to temperate species. The observed rapid change in the polar climate, especially warming, has created increased research interest to discover the underlying causes and potential consequences on single species to entire ecosystems. Next-Generation Sequencing (NGS) technologies have greatly expanded our knowledge by revealing the molecular underpinnings of physiological adaptations to polar environmental conditions. Their genomes, transcriptomes, and proteomes together with the first eukaryotic meta-omics data of surface ocean polar microbiomes reflect the environmental pressures through adaptive responses such as the expansion of protein families over time as a consequence of selection. Polar regions and their microbiomes are inherently connected to climate cycles and their feedback loops. An integrated understanding built on “omics” resources centered around diatoms as key primary producers will enable us to reveal unifying concepts of microbial co-evolution and adaptation in polar oceans. This knowledge, which aims to relate past environmental changes to specific adaptations, will be required to improve climate prediction models for polar ecosystems because it provides a unifying framework of how interacting and co-evolving biological communities might respond to future environmental change

Supporting families managing childhood eczema:Developing and optimising Eczema Care Online using qualitative research

Background: childhood eczema is often poorly controlled due to under-use of emollients and topical corticosteroids. Parents/carers report practical and psychosocial barriers to managing their child’s eczema, including child resistance. Online interventions could potentially support parents/carers; however, rigorous research developing such interventions has been limited. Aim: to develop an online behavioural intervention to help parents/carers manage and co-manage their child’s eczema. Design and setting: Intervention development using a theory-, evidence- and Person-Based Approach with qualitative research. Methods: a systematic review and qualitative synthesis (32 studies) and interviews with parents/carers (N=30) were used to identify barriers and facilitators to effective eczema management, and a prototype intervention was developed. Think-aloud interviews with parents/carers (N=25) were then used to optimise the intervention to increase its acceptability and feasibility. Results: qualitative research identified that parents/carers had concerns about using emollients and topical corticosteroids; incomplete knowledge and skills around managing eczema; and reluctance to transitioning to co-managing eczema with their child. Think-aloud interviews highlighted that while experienced parents/carers felt they knew how to manage eczema, some information about how to use treatments was still new. Techniques for addressing barriers included: providing a rationale explaining how emollients and topical corticosteroids work; demonstrating how to use treatments; and highlighting that the intervention provided new, up-to-date information. Conclusions: parents/carers need support in effectively managing and co-managing their child’s eczema. The key output of this research is Eczema Care Online (ECO) for Families; an online intervention for parents/carers of children with eczema, which is being evaluated in a randomised trial

Safety of topical corticosteroids in atopic eczema:an umbrella review

Objective: An umbrella review summarising all safety data from systematic reviews of topical corticosteroids (TCS) in adults and children with atopic eczema .Methods: Embase, MEDLINE, PubMed, Cochrane Database of Systematic Reviews and the Centre of Evidence Based Dermatology map of eczema systematic reviews searched until 7th November 2018 and Epistemonikos until 2nd March 2021. Reviews were included if they assessed safety of TCS in atopic eczema and searched >1 database using a reproducible search strategy. Review quality assessed using AMSTAR-2. PROSPERO registration: CRD42018079409. Results: 38 systematic reviews included, 34 low/critically low quality. Treatment and follow-up usually short (2-4 weeks). Key findings: TCS versus emollient/vehicle: No meta-analyses identified for skin-thinning. Two 2-week randomised controlled trials (RCTs) found no significant increased risk with very potent TCS (0/196 TCS vs 0/33 vehicle in children and 6/109 TCS vs 2/50 vehicle, age unknown). Biochemical adrenal suppression (cortisol) was 3.8% (95% CI 2.4%-5.8%) in a meta-analysis of 11 uncontrolled observational studies (any potency TCS, 522 children). Effects reversed when treatment ceased. TCS versus topical calcineurin inhibitors (TCIs): Meta-analysis showed higher relative risk of skin-thinning with TCS (RR 4.86, 95% CI 1.06-22.28, n=4128, four RCTs, including one 5-year RCT). Eight cases in 2068 participants, 7 using potent TCS. No evidence of growth suppression.Once daily versus more frequent TCS: No meta-analyses identified. No skin-thinning in one RCT (3 weeks potent TCS, n=94) or biochemical adrenal suppression in two RCTs (up to 2 weeks very potent/moderate TCS, n=129).TCS twice/week to prevent flares (‘weekend therapy’) versus vehicle: No meta-analyses identified. No evidence of skin-thinning in five RCTs. One RCT found biochemical adrenal suppression (2/44 children, potent TCS).Conclusions: We found no evidence of harm when TCS used intermittently “as required” to treat flares or “weekend therapy” to prevent flares. However, long-term safety data was limited

Different strategies for using topical corticosteroids in people with eczema

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: To establish the effectiveness and safety of different ways of using topical corticosteroids in people with eczema

Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild.

Evolutionary adaptation is generally thought to occur through incremental mutational steps, but large mutational leaps can occur during its early stages. These are challenging to study in nature due to the difficulty of observing new genetic variants as they arise and spread, but characterizing their genomic dynamics is important for understanding factors favoring rapid adaptation. Here, we report genomic consequences of recent, adaptive song loss in a Hawaiian population of field crickets (Teleogryllus oceanicus). A discrete genetic variant, flatwing, appeared and spread approximately 15 years ago. Flatwing erases sound-producing veins on male wings. These silent flatwing males are protected from a lethal, eavesdropping parasitoid fly. We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a flatwing quantitative trait locus covering a large region of the X chromosome. Gene expression profiling showed that flatwing is associated with extensive genome-wide effects on embryonic gene expression. We found that flatwing male crickets express feminized chemical pheromones. This male feminizing effect, on a different sexual signaling modality, is genetically associated with the flatwing genotype. Our findings suggest that the early stages of evolutionary adaptation to extreme pressures can be accompanied by greater genomic and phenotypic disruption than previously appreciated, and highlight how abrupt adaptation might involve suites of traits that arise through pleiotropy or genomic hitchhiking

Eczema Care Online: development and qualitative optimisation of an online behavioural intervention to support self-management in young people with eczema.

OBJECTIVES: To describe the development of Eczema Care Online (ECO), an online behaviour change intervention for young people with eczema (phase I); and explore and optimise the acceptability of ECO among this target group using think-aloud interviews (phase II). METHODS: Theory-based, evidence-based and person-based approaches to intervention development were used. In phase I, a qualitative systematic review and qualitative interviews developed an in-depth understanding of the needs and challenges of young people with eczema. Guiding principles highlighted key intervention design objectives and features to address the needs of this target group to maximise user engagement. Behavioural analysis and logic modelling developed ECO's hypothesised programme theory. In phase II, qualitative think-aloud interviews were carried out with 28 young people with eczema and the intervention was optimised based on their feedback. RESULTS: The final intervention aimed to reduce eczema severity by supporting treatment use (emollients, topical corticosteroids/topical calcineurin inhibitors), management of irritants/triggers, emotional management and reducing scratching. Generally, young people expressed positive views of intervention content and design in think-aloud interviews. Quotes and stories from other young people with eczema and ECO's focus on living with eczema (not just topical treatments) were valuable for normalising eczema. Young people believed ECO addressed knowledge gaps they had from childhood and the safety information about topical corticosteroids was reassuring. Negative feedback was used to modify ECO. CONCLUSIONS: A prototype of the ECO intervention was developed using rigorous and complementary intervention development approaches. Subsequent think-aloud interviews helped optimise the intervention, demonstrated ECO is likely to be acceptable to this target group, and provided support for our guiding principles including key design objectives and features to consider when developing interventions for this population. A randomised controlled trial and process evaluation of the intervention is underway to assess effectiveness and explore user engagement with the intervention's behavioural goals

Strategies for using topical corticosteroids in children and adults with eczema.

BACKGROUND: Eczema is a common skin condition. Although topical corticosteroids have been a first-line treatment for eczema for decades, there are uncertainties over their optimal use. OBJECTIVES: To establish the effectiveness and safety of different ways of using topical corticosteroids for treating eczema. SEARCH METHODS: We searched databases to January 2021 (Cochrane Skin Specialised Register; CENTRAL; MEDLINE; Embase; GREAT) and five clinical trials registers. We checked bibliographies from included trials to identify further trials. SELECTION CRITERIA: Randomised controlled trials in adults and children with eczema that compared at least two strategies of topical corticosteroid use. We excluded placebo comparisons, other than for trials that evaluated proactive versus reactive treatment. DATA COLLECTION AND ANALYSIS: We used standard Cochrane methods, with GRADE certainty of evidence for key findings. Primary outcomes were changes in clinician-reported signs and relevant local adverse events. Secondary outcomes were patient-reported symptoms and relevant systemic adverse events. For local adverse events, we prioritised abnormal skin thinning as a key area of concern for healthcare professionals and patients. MAIN RESULTS: We included 104 trials (8443 participants). Most trials were conducted in high-income countries (81/104), most likely in outpatient or other hospital settings. We judged only one trial to be low risk of bias across all domains. Fifty-five trials had high risk of bias in at least one domain, mostly due to lack of blinding or missing outcome data. Stronger-potency versus weaker-potency topical corticosteroids Sixty-three trials compared different potencies of topical corticosteroids: 12 moderate versus mild, 22 potent versus mild, 25 potent versus moderate, and 6 very potent versus potent. Trials were usually in children with moderate or severe eczema, where specified, lasting one to five weeks. The most reported outcome was Investigator Global Assessment (IGA) of clinician-reported signs of eczema. We pooled four trials that compared moderate- versus mild-potency topical corticosteroids (420 participants). Moderate-potency topical corticosteroids probably result in more participants achieving treatment success, defined as cleared or marked improvement on IGA (52% versus 34%; odds ratio (OR) 2.07, 95% confidence interval (CI) 1.41 to 3.04; moderate-certainty evidence). We pooled nine trials that compared potent versus mild-potency topical corticosteroids (392 participants). Potent topical corticosteroids probably result in a large increase in number achieving treatment success (70% versus 39%; OR 3.71, 95% CI 2.04 to 6.72; moderate-certainty evidence). We pooled 15 trials that compared potent versus moderate-potency topical corticosteroids (1053 participants). There was insufficient evidence of a benefit of potent topical corticosteroids compared to moderate topical corticosteroids (OR 1.33, 95% CI 0.93 to 1.89; moderate-certainty evidence). We pooled three trials that compared very potent versus potent topical corticosteroids (216 participants). The evidence is uncertain with a wide confidence interval (OR 0.53, 95% CI 0.13 to 2.09; low-certainty evidence). Twice daily or more versus once daily application We pooled 15 of 25 trials in this comparison (1821 participants, all reported IGA). The trials usually assessed adults and children with moderate or severe eczema, where specified, using potent topical corticosteroids, lasting two to six weeks. Applying potent topical corticosteroids only once a day probably does not decrease the number achieving treatment success compared to twice daily application (OR 0.97, 95% CI 0.68 to 1.38; 15 trials, 1821 participants; moderate-certainty evidence). Local adverse events Within the trials that tested 'treating eczema flare-up' strategies, we identified only 26 cases of abnormal skin thinning from 2266 participants (1% across 22 trials). Most cases were from the use of higher-potency topical corticosteroids (16 with very potent, 6 with potent, 2 with moderate and 2 with mild). We assessed this evidence as low certainty, except for very potent versus potent topical corticosteroids, which was very low-certainty evidence.  Longer versus shorter-term duration of application for induction of remission No trials were identified. Twice weekly application (weekend, or 'proactive therapy') to prevent relapse (flare-ups) versus no topical corticosteroids/reactive application Nine trials assessed this comparison, generally lasting 16 to 20 weeks. We pooled seven trials that compared weekend (proactive) topical corticosteroids therapy versus no topical corticosteroids (1179 participants, children and adults with a range of eczema severities, though mainly moderate or severe). Weekend (proactive) therapy probably results in a large decrease in likelihood of a relapse from 58% to 25% (risk ratio (RR) 0.43, 95% CI 0.32 to 0.57; 7 trials, 1149 participants; moderate-certainty evidence). Local adverse events We did not identify any cases of abnormal skin thinning in seven trials that assessed skin thinning (1050 participants) at the end of treatment. We assessed this evidence as low certainty. Other comparisons  Other comparisons included newer versus older preparations of topical corticosteroids (15 trials), cream versus ointment (7 trials), topical corticosteroids with wet wrap versus no wet wrap (6 trials), number of days per week applied (4 trials), different concentrations of the same topical corticosteroids (2 trials), time of day applied (2 trials), topical corticosteroids alternating with topical calcineurin inhibitors versus topical corticosteroids alone (1 trial), application to wet versus dry skin (1 trial) and application before versus after emollient (1 trial). No trials compared branded versus generic topical corticosteroids and time between application of emollient and topical corticosteroids. AUTHORS' CONCLUSIONS: Potent and moderate topical corticosteroids are probably more effective than mild topical corticosteroids, primarily in moderate or severe eczema; however, there is uncertain evidence to support any advantage of very potent over potent topical corticosteroids. Effectiveness is similar between once daily and twice daily (or more) frequent use of potent topical corticosteroids to treat eczema flare-ups, and topical corticosteroids weekend (proactive) therapy is probably better than no topical corticosteroids/reactive use to prevent eczema relapse (flare-ups). Adverse events were not well reported and came largely from low- or very low-certainty, short-term trials. In trials that reported abnormal skin thinning, frequency was low overall and increased with increasing potency. We found no trials on the optimum duration of treatment of a flare, branded versus generic topical corticosteroids, and time to leave between application of topical corticosteroids and emollient. There is a need for longer-term trials, in people with mild eczema

Clinical outcomes and response to treatment of patients receiving topical treatments for pyoderma gangrenosum: a prospective cohort study

Background: pyoderma gangrenosum (PG) is an uncommon dermatosis with a limited evidence base for treatment. Objective: to estimate the effectiveness of topical therapies in the treatment of PG. Methods: prospective cohort study of UK secondary care patients with a clinical diagnosis of PG suitable for topical treatment (recruited July 2009 to June 2012). Participants received topical therapy following normal clinical practice (mainly Class I-III topical corticosteroids, tacrolimus 0.03% or 0.1%). Primary outcome: speed of healing at 6 weeks. Secondary outcomes: proportion healed by 6 months; time to healing; global assessment; inflammation; pain; quality-of-life; treatment failure and recurrence. Results: Sixty-six patients (22 to 85 years) were enrolled. Clobetasol propionate 0.05% was the most commonly prescribed therapy. Overall, 28/66 (43.8%) of ulcers healed by 6 months. Median time-to-healing was 145 days (95% CI: 96 days, ∞). Initial ulcer size was a significant predictor of time-to-healing (hazard ratio 0.94 (0.88;80 1.00); p = 0.043). Four patients (15%) had a recurrence. Limitations: No randomised comparator Conclusion: Topical therapy is potentially an effective first-line treatment for PG that avoids possible side effects associated with systemic therapy. It remains unclear whether more severe disease will respond adequately to topical therapy alone

Investigating the Effect of Conflicting Goals and Transparency on Trust and Collaboration in Multi-Team Systems

In Air Traffic Management (ATM) multiple teams have to collaborate to achieve efficient and safe operation. Multiple-team operations rely on communication and information sharing between the team members. In this field, multi-team systems (MTSs) are the most common form of organization. The interface between the organizations involved (e.g. air traffic control, cockpit crews, airports) is of central importance. Apart from a common goal, different stakeholders may pursue individual goals governed by their own company culture or policies. Therefore, simply sharing all available information may not be enough to ensure safe and efficient operation. As part of the project ITC (Inter-Team Collaboration), an experimental study with 48 teams of three (n=144) has just started to investigate the impact that conflicting goals have on communication and collaboration. Additionally, it examines whether and how transparency in roles, processes, and goals can affect performance, communication, and trust in multi-team systems. In the synthetic task environment (STE) ConCenT (Control Center Task Environment), teams of three have to collaborate to detect system failures in time, determine their causes, and decide on a solution in order to ensure successful production processes. Measurements of performance, perceived trust, communication, and gaze data will be analyzed to examine and compare different coordination and communication patterns on a group level. Results of the study will identify factors that may facilitate or hinder collaborative work processes in an MTS, thus enabling the validation of an approach to improve collaboration through transparency and mutual trust