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Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.

Automobility centred on private car use generates various externalities – or 'antagonisms' – that threaten its sustainability as a mobility regime. Through expanding the practice and spaces of driving, mass immobility can result. With increased car use, comes increased energy use, generating an ecological antagonism for this regime. Finally, greater car use has resulted in mass road traffic injuries and fatalities, which presents another threat to the growth and maintenance of this unique form of automobility. While these antagonisms present a risk, they have also been leveraged as a means to establish and secure the dominance of automobility. As part of a wider study exploring discourses of opposition to redistributive active travel measures in Dún Laoghaire-Rathdown, Ireland, this paper illustrates how active travel measures that present a challenge to automobility are depicted as disruptive, dangerous and dirty. These measures, precisely designed to mitigate the antagonisms of mass car use, are construed instead as primary causes of these systemic externalities. This study thereby reveals how active travel spaces themselves – and spatial regulations that favour active travellers – can be unfavourably represented as a means of politically sustaining automobility. [ABSTRACT FROM AUTHOR]

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

Car-based automobility remains dominant across Europe despite the high energy requirements such a system embeds. This system is becoming increasingly problematised. As part of an alternative vision for everyday mobility, an aspiration for vélomobility appears to be growing. In light of the persistent subordinate status of cycling across much of Europe relative to driving, attempts to lay the foundations for everyday cycling are often pursued through the implementation of redistributive cycleways and broader public space measures that prioritise active travel. These important attempts to change public space can be blocked through public opposition, which can feature as part of broader social practices that may politically sustain automobility as a dominant system. In this study, we explore how automobility is politically sustained in discourses of opposition to a major active travel scheme proposal in the context of Dún Laoghaire-Rathdown, Ireland. We uncover how a normatively car-centric discourse of everyday mobility constructs driving as the essential mobility practice for the functional tasks of everyday life, while cycling is relegated to recreational and conditional mobility, and briefly consider how an alternative discourse of everyday mobility that decentres the car may be advanced. [ABSTRACT FROM AUTHOR]

Background: Susac syndrome is a vasculopathy, resulting in the classic triad of branch retinal artery occlusion (BRAO), inner ear ischemia, and brain ischemia. In this retrospective chart review, we characterize fluorescein angiography (FA) findings and other ancillary studies in Susac syndrome, including the appearance of persistent disease activity and the occurrence of new subclinical disease on FA. Methods: This multicenter, retrospective case series was institutional review board--approved and included patients with the complete triad of Susac syndrome evaluated with FA, contrasted MRI of the brain, and audiometry from 2010 to 2020. The medical records were reviewed for these ancillary tests, along with demographics, symptoms, visual acuity, visual field defects, and findings on fundoscopy. Clinical relapse was defined as any objective evidence of disease activity during the follow-up period after initial induction of clinical quiescence. The main outcome measure was the sensitivity of ancillary testing, including FA, MRI, and audiometry, to detect relapse. Results: Twenty of the 31 (64%) patients had the complete triad of brain, retinal, and vestibulocochlear involvement from Susac syndrome and were included. Median age at diagnosis was 43.5 years (range 21--63), and 14 (70%) were women. Hearing loss occurred in 20 (100%), encephalopathy in 13 (65%), vertigo in 15 (75%), and headaches in 19 (95%) throughout the course of follow-up. Median visual acuity at both onset and final visit was 20/20 in both eyes. Seventeen (85%) had BRAO at baseline, and 10 (50%) experienced subsequent BRAO during follow-up. FA revealed nonspecific leakage from previous arteriolar damage in 20 (100%), including in patients who were otherwise in remission. Of the 11 episodes of disease activity in which all testing modalities were performed, visual field testing/fundoscopy was abnormal in 4 (36.4%), MRI brain in 2 (18.2%), audiogram in 8 (72.7%), and FA in 9 (81.8%). Conclusions: New leakage on FA is the most sensitive marker of active disease. Persistent leakage represents previous damage, whereas new areas of leakage suggest ongoing disease activity that requires consideration of modifying immunosuppressive therapy. [ABSTRACT FROM AUTHOR]

In the field of cycling studies, explicit and implicit theories of risk are frequently used for the purposes of research design, data collection, data analysis, and policy. In this article, we argue that this field may benefit from theories and concepts that speak to – but go beyond – theories of risk, and more directly focus on matters of right and recognition. Drawing on grounded theory research involving interviews with 28 cyclists in Dublin, Ireland, we analyse the 'risk talk' from five participant accounts through an application of the rights-orientated perspective of precarious entitlement theory. We argue for its utility as a theory, specifically as a complementary alternative to risk-focused approaches. First, we illustrate how precarious entitlement goes beyond the conceptual limits of understanding cycling experience from perspectives of 'risk' and 'safety', by consolidating a concern with 'right' and 'risk'. Second, we illustrate how interpreting particular cycling practices as patterns of submission and social struggle (privatising vulnerability and provoking responsibility) can transcend individualised interpretations of such practices as 'risk management' and 'risk-taking'. In the discussion, we consider the value of this theory in relation to existing research in this field, with reference to socio-cultural risk theory. In conclusion, we argue for a more transparently rights-based approach to cycle policy in light of the dominance of a specific variety of risk discourse that arguably obscures a consideration of rights to use public space and what a realisation of such rights might require from both the public and the state. [ABSTRACT FROM AUTHOR]