Open-source single-particle analysis for super-resolution microscopy with virusmapper

Super-resolution fluorescence microscopy is currently revolutionizing cell biology research. Its capacity to break the resolution limit of around 300 nm allows for the routine imaging of nanoscale biological complexes and processes. This increase in resolution also means that methods popular in electron microscopy, such as single-particle analysis, can readily be applied to super-resolution fluorescence microscopy. By combining this analytical approach with super-resolution optical imaging, it becomes possible to take advantage of the molecule-specific labeling capacity of fluorescence microscopy to generate structural maps of molecular elements within a metastable structure. To this end, we have developed a novel algorithm - VirusMapper - packaged as an easy-to-use, high-performance, and high-throughput ImageJ plugin. This article presents an in-depth guide to this software, showcasing its ability to uncover novel structural features in biological molecular complexes. Here, we present how to assemble compatible data and provide a step-by-step protocol on how to use this algorithm to apply single-particle analysis to super-resolution images

Evidence for a lava lake on Mt. Michael volcano, Saunders Island (South Sandwich Islands) from Landsat, Sentinel-2 and ASTER satellite imagery

Mt. Michael is an active stratovolcano on Saunders Island in the South Sandwich Islands; a remote, oceanic island arc in the southern Atlantic Ocean, bordering the Southern Ocean. The arc contains the only active volcanoes in the South Georgia and South Sandwich Islands British Overseas Territory, yet little is known of their activity. Despite lava lakes being extremely rare with only a few global examples, previous analyses of satellite AVHRR imagery of Mt. Michael in the 1990s showed persistent thermal anomalies not associated with magma overflowing the crater. This suggested the existence of a lava lake inside Mt. Michael's crater. However, their study relied on 1 km resolution imagery, and there have been no long-term investigations to determine if this is a persistent feature

Cognitive training as a resolution for early executive function difficulties in children with intellectual disabilities

Core executive functions (EF) such as attention, and working memory have been strongly associated with academic achievement, language development and behavioral stability. In the case of children who are vulnerable to cognitive and learning problems because of an underlying intellectual disability, EF difficulties will likely exacerbate an already compromised cognitive system. The current review examines cognitive training programs that aim to improve EF, specifically focusing on the potential of this type of intervention for children who have intellectual disabilities. We conclude that despite considerable discrepancies regarding reported intervention effects, these inconsistencies can be attributed to flaws in both program and study design. We discuss the steps needed to address these limitations and to facilitate the advancement of non-pharmaceutical interventions for children with intellectual disabilities

Data acquisition system for the MuLan muon lifetime experiment

We describe the data acquisition system for the MuLan muon lifetime experiment at Paul Scherrer Institute. The system was designed to record muon decays at rates up to 1 MHz and acquire data at rates up to 60 MB/sec. The system employed a parallel network of dual-processor machines and repeating acquisition cycles of deadtime-free time segments in order to reach the design goals. The system incorporated a versatile scheme for control and diagnostics and a custom web interface for monitoring experimental conditions.Comment: 19 pages, 8 figures, submitted to Nuclear Instruments and Methods

The association between driving time and unhealthy lifestyles: a cross-sectional, general population study of 386 493 UK Biobank participants

Background: Driving is a common type of sedentary behaviour; an independent risk factor for poor health. The study explores whether driving is also associated with other unhealthy lifestyle factors. Methods: In a cross-sectional study of UK Biobank participants, driving time was treated as an ordinal variable and other lifestyle factors dichotomized into low/high risk based on guidelines. The associations were explored using chi-square tests for trend and binary logistic regression. Results: Of the 386 493 participants who drove, 153 717 (39.8%) drove <1 h/day; 140 140 (36.3%) 1 h/day; 60 973 (15.8%) 2 h/day; and 31 663 (8.2%) ≥3 h/day. Following adjustment for potential confounders, driving ≥3 h/day was associated with being overweight/obese (OR = 1.74, 95% CI: 1.64–1.85), smoking (OR = 1.48, 95% CI: 1.37–1.63), insufficient sleep (1.70, 95% CI: 1.61–1.80), low fruit/vegetable intake (OR = 1.26, 95% CI: 1.18–1.35) and low physical activity (OR = 1.05, 95% CI: 1.00–1.11), with dose relationships for the first three, but was not associated with higher alcohol consumption (OR = 0.94, 95% CI: 0.87–1.02). Conclusions: Sedentary behaviour, such as driving, is known to have an independent association with adverse health outcomes. It may have additional impact mediated through its effect on other aspects of lifestyle. People with long driving times are at higher risk and might benefit from targeted interventions

Backreacted T-folds and non-geometric regions in configuration space

We provide the backreaction of the T-fold doubly T-dual to a background with NSNS three-form flux on a three-torus. We extend the backreacted T-fold to include cases with a flux localized in one out of three directions. We analyze the resulting monodromy domain walls and vortices. In these backgrounds, we give an analysis of the action of T-duality on observables like charges and Wilson surfaces. We analyze arguments for the existence of regions in the configuration space of second quantized string theory that cannot be reduced to geometry. Finally, by allowing for space-dependent moduli, we find a supergravity solution which is a T-fold with hyperbolic monodromies.Comment: 25 pages, 4 figures; v2: minor changes, reference adde

Site investigation for the effects of vegetation on ground stability

The procedure for geotechnical site investigation is well established but little attention is currently given to investigating the potential of vegetation to assist with ground stability. This paper describes how routine investigation procedures may be adapted to consider the effects of the vegetation. It is recommended that the major part of the vegetation investigation is carried out, at relatively low cost, during the preliminary (desk) study phase of the investigation when there is maximum flexibility to take account of findings in the proposed design and construction. The techniques available for investigation of the effects of vegetation are reviewed and references provided for further consideration. As for general geotechnical investigation work, it is important that a balance of effort is maintained in the vegetation investigation between (a) site characterisation (defining and identifying the existing and proposed vegetation to suit the site and ground conditions), (b) testing (in-situ and laboratory testing of the vegetation and root systems to provide design parameters) and (c) modelling (to analyse the vegetation effects)

No ‘silver bullet’:Multiple factors control population dynamics of european purple sea urchins in Lough Hyne marine reserve, Ireland

Two-decade-long monitoring studies at Europe\u27s first statutory marine reserve—Lough Hyne in SW Ireland—indicate that benthic communities are rapidly changing. Populations of the ecologically important purple urchin (Paracentrotus lividus) have fluctuated widely, most recently with a population boom in the late 1990s, followed by a mass mortality that persists to the present day. Eight general hypotheses have been proposed to account for the urchin decline including cold temperature limiting reproduction, ephemeral algal exudates disrupting urchin fertilization, low larval availability (due to over-harvesting and/or episodic recruitment), high mortality of settlers and juveniles due to hypoxia, hyperoxia, or predation (a trophic cascade hypothesis), and increased mortality due to pathogens (stress hypothesis). The cold-temperature and the trophic cascade hypotheses appear unlikely. The remaining hypotheses, however, all seem to play a role, to some degree, in driving the urchin decline. Ulvoid exudates, for example, significantly reduced urchin fertilization and few larvae were found in plankton tows (2012–2015), indicating low larval availability in summer. Whilst settling urchins regularly recruited under shallow-subtidal rocks until 2011, no settlers were found in these habitats from 2011 to 2014 or in field experiments (2012–2018) using various settlement substrata. Seawater quality was poor in shallow areas of the lough with extreme oxygen fluctuations (diel-cycling hypoxia), and 1-day experimental exposures to DO values < 1 mg L−1 were lethal to most juvenile urchins. Multiple increases of the predatory spiny starfish (Marthasterias glacialis) population in recent decades may also have contributed to the demise of the coexisting juvenile urchins. Finally, urchins of all sizes were seen suffering from dropped spines, tissue necrosis, or white-coloured infection, suggestive of stress-related pathogen mortality. There was a paucity of broken tests, indicating limited predation by large crustaceans; the large number of adult urchins ‘missing’ and few P. lividus tests on the north shore points to possible urchin removal by poachers and/or starfish predation. While these ecological, environmental, and anthropogenic processes occur on open coast rocky shores, many are exacerbated by the semi-enclosed nature of this fully marine sea lough due to its limited flushing. Multiple factors, including low larval availability and rapidly expanding starfish populations, coupled with degraded habitat quality (ephemeral algal mats and extreme oxygen fluctuations), indicate that the purple urchin populations will not recover without an improvement in the water quality of Lough Hyne Marine Reserve, the restocking of urchins, and protection from poaching

Associations of dietary protein intake with fat free mass and grip strength: cross-sectional study in 146,816 UK Biobank participants

Adequate dietary protein intake is important for the maintenance of fat-free mass (FFM) and muscle strength: optimal requirements remain unknown. The aim of the current study was to explore the associations of protein intake with FFM and grip strength. We used baseline data from the UK Biobank (146,816 participants aged 40-69 years with data collected 2007-2010 across the UK) to examine the associations of protein intake with FFM and grip strength. Protein intake was positively associated with FFM (men 5.1% [95% CI: 5.0; 5.2] and women 7.7% [95% CI: 7.7; 7.8]) and grip strength (men 0.076 kg/kg [95% CI: 0.074; 0.078] and women 0.074 kg/kg [95% CI: 0.073; 0.076]) per 0.5 grams per kg body mass per day (g/kg/day) increment in protein intake. FFM and grip strength were higher with higher intakes across the full range of intakes, i.e. highest in those reporting consuming &gt; 2.0 g/grams per kg/day independently of socio-demographics, other dietary measures, physical activity and comorbidities. FFM and grip strength were lower with age, but this association did not differ by protein intake categories (P &gt; 0.05). Current recommendation for all adults (40-69 years) for protein intake (0.8 grams per kg body mass per day) may need to be increased to optimise FFM and grip strength