Models of Individual Blue Stragglers

This chapter describes the current state of models of individual blue stragglers. Stellar collisions, binary mergers (or coalescence), and partial or ongoing mass transfer have all been studied in some detail. The products of stellar collisions retain memory of their parent stars and are not fully mixed. Very high initial rotation rates must be reduced by an unknown process to allow the stars to collapse to the main sequence. The more massive collision products have shorter lifetimes than normal stars of the same mass, while products between low mass stars are long-lived and look very much like normal stars of their mass. Mass transfer can result in a merger, or can produce another binary system with a blue straggler and the remnant of the original primary. The products of binary mass transfer cover a larger portion of the colour-magnitude diagram than collision products for two reasons: there are more possible configurations which produce blue stragglers, and there are differing contributions to the blended light of the system. The effects of rotation may be substantial in both collision and merger products, and could result in significant mixing unless angular momentum is lost shortly after the formation event. Surface abundances may provide ways to distinguish between the formation mechanisms, but care must be taking to model the various mixing mechanisms properly before drawing strong conclusions. Avenues for future work are outlined.Comment: Chapter 12, in Ecology of Blue Straggler Stars, H.M.J. Boffin, G. Carraro & G. Beccari (Eds), Astrophysics and Space Science Library, Springe

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t

Public behaviour in response to perceived hostile threats: An evidence base and guide for practitioners and policymakers

Background: Public behaviour and the new hostile threats • Civil contingencies planning and preparedness for hostile threats requires accurate and up to date knowledge about how the public might behave in relation to such incidents. Inaccurate understandings of public behaviour can lead to dangerous and counterproductive practices and policies. • There is consistent evidence across both hostile threats and other kinds of emergencies and disasters that significant numbers of those affected give each other support, cooperate, and otherwise interact socially within the incident itself. • In emergency incidents, competition among those affected occurs in only limited situations, and loss of behavioural control is rare. • Spontaneous cooperation among the public in emergency incidents, based on either social capital or emergent social identity, is a crucial part of civil contingencies planning. • There has been relatively little research on public behaviour in response to the new hostile threats of the past ten years, however. • The programme of work summarized in this briefing document came about in response to a wave of false alarm flight incidents in the 2010s, linked to the new hostile threats (i.e., marauding terrorist attacks). • By using a combination of archive data for incidents in Great Britain 2010-2019, interviews, video data analysis, and controlled experiments using virtual reality technology, we were able to examine experiences, measure behaviour, and test hypotheses about underlying psychological mechanisms in both false alarms and public interventions against a hostile threat. Re-visiting the relationship between false alarms and crowd disasters • The Bethnal Green tube disaster of 1943, in which 173 people died, has historically been used to suggest that (mis)perceived hostile threats can lead to uncontrolled ‘stampedes’. • Re-analysis of witness statements suggests that public fears of Germany bombs were realistic rather than unreasonable, and that flight behaviour was socially structured rather than uncontrolled. • Evidence for a causal link between the flight of the crowd and the fatal crowd collapse is weak at best. • Altogether, the analysis suggests the importance of examining people’s beliefs about context to understand when they might interpret ambiguous signals as a hostile threat, and that. Tthe concepts of norms and relationships offer better ways to explain such incidents than ‘mass panic’. Why false alarms occur • The wider context of terrorist threat provides a framing for the public’s perception of signals as evidence of hostile threats. In particular, the magnitude of recent psychologically relevant terrorist attacks predicts likelihood of false alarm flight incidents. • False alarms in Great Britain are more likely to occur in those towns and cities that have seen genuine terrorist incidents. • False alarms in Great Britain are more likely to occur in the types of location where terrorist attacks happen, such as shopping areass, transport hubs, and other crowded places. • The urgent or flight behaviour of other people (including the emergency services) influences public perceptions that there is a hostile threat, particularly in situations of greater ambiguity, and particularly when these other people are ingroup. • High profile tweets suggesting a hostile threat, including from the police, have been associated with the size and scale of false alarm responses. • In most cases, it is a combination of factors – context, others’ behaviour, communications – that leads people to flee. A false alarm tends not to be sudden or impulsive, and often follows an initial phase of discounting threat – as with many genuine emergencies. 2.4 How the public behave in false alarm flight incidents • Even in those false alarm incidents where there is urgent flight, there are also other behaviours than running, including ignoring the ‘threat’, and walking away. • Injuries occur but recorded injuries are relatively uncommon. • Hiding is a common behaviour. In our evidence, this was facilitated by orders from police and offers from people staff in shops and other premises. • Supportive behaviours are common, including informational and emotional support. • Members of the public often cooperate with the emergency services and comply with their orders but also question instructions when the rationale is unclear. • Pushing, trampling and other competitive behaviour can occur,s but only in restricted situations and briefly. • At the Oxford Street Black Friday 2017 false alarm, rather than an overall sense of unity across the crowd, camaraderie existed only in pockets. This was likely due to the lack of a sense of common fate or reference point across the incident; the fragmented experience would have hindered the development of a shared social identity across the crowd. • Large and high profile false alarm incidents may be associated with significant levels of distress and even humiliation among those members of the public affected, both at the time and in the aftermath, as the rest of society reflects and comments on the incident. Public behaviour in response to visible marauding attackers • Spontaneous, coordinated public responses to marauding bladed attacks have been observed on a number of occasions. • Close examination of marauding bladed attacks suggests that members of the public engage in a wide variety of behaviours, not just flight. • Members of the public responding to marauding bladed attacks adopt a variety of complementary roles. These, that may include defending, communicating, first aid, recruiting others, marshalling, negotiating, risk assessment, and evidence gathering. Recommendations for practitioners and policymakers • Embed the psychology of public behaviour in emergencies in your training and guidance. • Continue to inform the public and promote public awareness where there is an increased threat. • Build long-term relations with the public to achieve trust and influence in emergency preparedness. • Use a unifying language and supportive forms of communication to enhance unity both within the crowd and between the crowd and the authorities. • Authorities and responders should take a reflexive approach to their responses to possible hostile threats, by reflecting upon how their actions might be perceived by the public and impact (positively and negatively) upon public behaviour. • To give emotional support, prioritize informative and actionable risk and crisis communication over emotional reassurances. • Provide first aid kits in transport infrastructures to enable some members of the public more effectively to act as zero responders

Sixty Years of Modern Human Origins in the American Anthropological Association

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65197/1/aa.2003.105.1.89.pd

Genomics-informed outbreak investigations of SARS-CoV-2 using civet

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different ’catchments’ and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1000 cases of unexplained pediatric hepatitis in children have been reported worldwide, including 278 cases in the UK 1. Here we report investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator subjects, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in liver, blood, plasma or stool from 27/28 cases. We found low levels of Adenovirus (HAdV) and Human Herpesvirus 6B (HHV-6B), in 23/31 and 16/23 respectively of the cases tested. In contrast, AAV2 was infrequently detected at low titre in blood or liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T-cells and B-lineage cells. Proteomic comparison of liver tissue from cases and healthy controls, identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and in severe cases HHV-6B, may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Genomics-informed outbreak investigations of SARS-CoV-2 using civet

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different ’catchments’ and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant