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There has been considerable focus on the main, expansionary, and inter-regionally linked or 'globalising' periods in Old World pre- and proto-history, with a focus on identifying, analyzing and dating collapse at the close of these pivotal periods. The end of the Early Bronze Age in the late third millennium BCE and a subsequent 'intermediate' or transitional period before the Middle Bronze Age (~2200-1900 BCE), and the end of the Late Bronze Age in the late second millennium BCE and the ensuing period of transformation during the Early Iron Age (~1200-900 BCE), are key examples. Among other issues, climate change is regularly invoked as a cause or factor in both cases. Recent considerations of \"collapse\" have emphasized the unpredictability and variability of responses during such periods of reorganization and transformation. Yet, a gap in scholarly attention remains in documenting the responses observed at important sites during these 'transformative' periods in the Old World region. Tell Tayinat in southeastern Turkey, as a major archaeological site occupied during these two major 'in between' periods of transformation, offers a unique case for comparing and contrasting differing responses to change. To enable scholarly assessment of associations between the local trajectory of the site and broader regional narratives, an essential preliminary need is a secure, resolved timeframe for the site. Here we report a large set of radiocarbon data and incorporate the stratigraphic sequence using Bayesian chronological modelling to create a refined timeframe for Tell Tayinat and a secure basis for analysis of the site with respect to its broader regional context and climate history.

Food availability influences multiple stages of the breeding cycle of birds, and supplementary feeding has helped in its understanding. Most supplementation studies have reported advancements of laying, whilst others, albeit less numerous, have also demonstrated fitness benefits such as larger clutches, shorter incubation periods, and greater hatching success. Relatively few studies, however, have investigated the effects of supplementary feeding for protracted periods across multiple stages of the breeding cycle. These effects are important to understand since long-term food supplementation of birds is recommended in urban habitats and is used as a tool to increase reproductive output in endangered species. Here, we compare the breeding phenology and productivity of blue tits Cyanistes caeruleus and great tits Parus major breeding in food-supplemented and non-supplemented blocks in a broadleaf woodland in central England over three seasons (2006-2008). Supplementation was provided continuously from several weeks pre-laying until hatching, and had multiple significant effects. Most notably, supplementation reduced brood size significantly in both species, by half a chick or more at hatching (after controlling for year and hatching date). Reduced brood sizes in supplemented pairs were driven by significantly smaller clutches in both species and, in blue tits, significantly lower hatching success. These are novel and concerning findings of food supplementation. As expected, supplementary feeding advanced laying and shortened incubation periods significantly in both species. We discuss the striking parallels between our findings and patterns in blue and great tit reproduction in urban habitats, and conclude that supplementary feeding may not always enhance the breeding productivity of birds.

Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires' disease. Previous genomic studies have shown that recombination accounts for a high proportion (>96%) of diversity within several major disease-associated sequence types (STs) of L. pneumophila. This suggests that recombination represents a potentially important force shaping adaptation and virulence. Despite this, little is known about the biological effects of recombination in L. pneumophila, particularly with regards to homologous recombination (whereby genes are replaced with alternative allelic variants). Using newly available population genomic data, we have disentangled events arising from homologous and non-homologous recombination in six major disease-associated STs of L. pneumophila (subsp. pneumophila), and subsequently performed a detailed characterisation of the dynamics and impact of homologous recombination. We identified genomic \"hotspots\" of homologous recombination that include regions containing outer membrane proteins, the lipopolysaccharide (LPS) region and Dot/Icm effectors, which provide interesting clues to the selection pressures faced by L. pneumophila. Inference of the origin of the recombined regions showed that isolates have most frequently imported DNA from isolates belonging to their own clade, but also occasionally from other major clades of the same subspecies. This supports the hypothesis that the possibility for horizontal exchange of new adaptations between major clades of the subspecies may have been a critical factor in the recent emergence of several clinically important STs from diverse genomic backgrounds. However, acquisition of recombined regions from another subspecies, L. pneumophila subsp. fraseri, was rarely observed, suggesting the existence of a recombination barrier and/or the possibility of ongoing speciation between the two subspecies. Finally, we suggest that multi-fragment recombination may occur in L. pneumophila, whereby multiple non-contiguous segments that originate from the same molecule of donor DNA are imported into a recipient genome during a single episode of recombination.

Legionnaires' disease is an important cause of community-acquired and hospital-acquired pneumonia. Although uncommon, Legionnaires' disease continues to cause disease outbreaks of public health significance. The disease is caused by any species of the Gram-negative aerobic bacteria belonging to the genus Legionella; Legionella pneumophila serogroup 1 is the causative agent of most cases in Europe. In this Review we outline the global epidemiology of Legionnaires' disease, summarise its diagnosis and management, and identify research gaps and priorities. Early clinical diagnosis and prompt initiation of appropriate antibiotics for Legionella spp in all patients with community-acquired or hospital-acquired pneumonias is a crucial measure for management of the disease. Progress in typing and sequencing technologies might additionally contribute to understanding the distribution and natural history of Legionnaires' disease, and inform outbreak investigations. Control of Legionnaires' disease outbreaks relies on rapid ascertainment of descriptive epidemiological data, combined with microbiological information to identify the source and implement control measures. Further research is required to define the actual burden of disease, factors that influence susceptibility, key sources of infection, and differences in virulence between strains of Legionella species. Other requirements are improved, specific, sensitive, and rapid diagnostic tests to accurately inform management of Legionnaires' disease, and controlled clinical trials to ascertain the optimum antibiotics for treatment.

Decisions that we make about email legitimacy can result in a pernicious threat to security of both individuals and organisations. Yet user response to phishing emails is far from uniform; some respond while others do not. What is the source of this diversity in decision-making? From a psychological perspective, we consider cognitive and situational influences that might explain why certain users are more susceptible than others. Alongside an email judgment task employed as a proxy for fraud susceptibility, 224 participants completed a range of cognitive tasks. In addition, we manipulated time pressure for email legitimacy judgments. We identify cognitive reflection and sensation seeking as significant, albeit modest, predictors of susceptibility. Further to this, participants asked to make quicker responses made more judgment errors. We conclude there are cognitive signatures that partially contribute to email fraud susceptibility, with implications for efforts to limit online security breaches and train secure behaviors.

Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective. This study describes the analysis of the S. pneumoniae capsular operon genetic sequence to determine serotype distinguishing features and the development, evaluation and verification of an automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT ( Pneumo coccal Ca psule T yping). Initially, WGS data from 871 S. pneumoniae isolates were mapped to reference cps locus sequences for the 92 serotypes. Thirty-two of 92 serotypes could be unambiguously identified based on sequence similarities within the cps operon. The remaining 60 were allocated to one of 20 ‘genogroups’ that broadly correspond to the immunologically defined serogroups. By comparing the cps reference sequences for each genogroup, unique molecular differences were determined for serotypes within 18 of the 20 genogroups and verified using the set of 871 isolates. This information was used to design a decision-tree style algorithm within the PneumoCaT bioinformatics tool to predict to serotype level for 89/94 (92 + 2 molecular types/subtypes) from WGS data and to serogroup level for serogroups 24 and 32, which currently comprise 2.1% of UK referred, invasive isolates submitted to the National Reference Laboratory (NRL), Public Health England (June 2014–July 2015). PneumoCaT was evaluated with an internal validation set of 2065 UK isolates covering 72/92 serotypes, including 19 non-typeable isolates and an external validation set of 2964 isolates from Thailand ( n = 2,531), USA ( n = 181) and Iceland ( n = 252). PneumoCaT was able to predict serotype in 99.1% of the typeable UK isolates and in 99.0% of the non-UK isolates. Concordance was evaluated in UK isolates where further investigation was possible; in 91.5% of the cases the predicted capsular type was concordant with the serologically derived serotype. Following retesting, concordance increased to 99.3% and in most resolved cases (97.8%; 135/138) discordance was shown to be caused by errors in original serotyping. Replicate testing demonstrated that PneumoCaT gave 100% reproducibility of the predicted serotype result. In summary, we have developed a WGS-based serotyping method that can predict capsular type to serotype level for 89/94 serotypes and to serogroup level for the remaining four. This approach could be integrated into routine typing workflows in reference laboratories, reducing the need for phenotypic immunological testing.

We hypothesize that in pediatric trauma patients, CT scans after normal chest x-rays do not add information that alters clinical decision making. A retrospective review of trauma patients < 15 years with chest imaging evaluated at a pediatric trauma center between 1/2013 and 6/2019 was performed. Imaging was reviewed for significant findings that could affect care. A guideline was established in January 2017 which emphasized x-rays prior to CTs and no CTs after normal x-rays. A prospective review was performed from 1/2017-6/2019. Pre and post guideline groups were compared. From 2013 to 2016, 246 patients met inclusion. 29.5% had a chest CT after a normal x-ray, only 1.8% (1/57) had a significant result. From 2017 to 2019, 188 patients were reviewed post guideline; only 9.4% received a CT after normal x-ray, of which 6.3% (1/16) were significant. Neither changed clinical management. Chest CT following normal chest x-ray does not change clinical management in pediatric trauma patients. Monitoring and education following guideline implementation improves long term outcomes. •In pediatric trauma, CTs after normal chest x-rays generally do not change management.•A radiation reduction guideline can lower the number of CT scans.•Continued education and monitoring after guideline implementation improve outcomes.•Monitoring and education are an important aspect of quality improvement.

•In April 2010 PCV7 was replaced by PCV13.•We investigated pneumococcal carriage in children and their household contacts.•Carriage of PCV13 serotypes rapidly reduced in vaccinated and unvaccinated.•Carriage rates in children remain unchanged.•Low case carrier rates of replacing serotypes should further reduce overall IPD. In April 2010 the 7-valent pneumococcal conjugate vaccine (PCV7) was replaced by the 13-valent PCV. We investigated pneumococcal carriage in children eligible for PCV7 or PCV13 and their household contacts. Eligible families in Hertfordshire and Gloucester were identified and a nasopharyngeal swab obtained from consenting household members between July 2012 and March 2013. Samples were cultured for Streptococcus pneumoniae and serotyped by standard methods. For each serotype the ratio of its prevalence in invasive pneumococcal disease (IPD) to its carriage prevalence (case:carrier ratio, CCR) was calculated. Results were compared with previous carriage studies in 2001/2002 and 2008/2009, before and after PCV7 introduction. 217 households were included. Among <5-year olds 47.7% (95% confidence interval 41.8–53.5) were carrying a pneumococcus compared with 51.0% (95% CI: 44.0–58.0) in 2008/2009 and 48.4% (95% CI: 44.1–52.7) in 2001/2002. The odds of carrying a PCV7 serotype was significantly reduced in 2008/2009 (0.07, 95% CI: 0.03–0.16) and 2012/2013 (0.01 95% CI: 0.00–0.07) relative to 2001/2002, while the odds of carrying any of the extra six PCV13 serotypes increased after PCV7 introduction (1.38, 95%CI: 0.73–2.59) but declined significantly after PCV13 introduction (0.05, 95%CI: 0.01–0.37). The CCRs for the frequently carried serotypes were relatively low, with the highest CCR observed for serotypes 7F, 19A, 3, 8, and 33F. Across the three carriage studies, CCR estimates were stable for nearly all serotypes. Carriage of additional PCV13 serotypes has rapidly reduced post-PCV13 introduction in both vaccinated and unvaccinated individuals with a continued decline in transmission of PCV7 serotypes. Carriage rates in children remain unchanged, but the low CCRs of replacing serotypes would be expected to further reduce overall IPD across all age groups.

Background During a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with comparison to isolates from patients with invasive disease (iGAS) to test the hypotheses that the increase in SF was due to either the introduction of one or more new/emerging strains in the population in England or the transmission of a known genetic element through the population of GAS by horizontal gene transfer (HGT) resulting in infections with an increased likelihood of causing SF. Isolates were collected to provide geographical representation, for approximately 5% SF isolates from each region from 1 st April 2014 to 18 th June 2014. Contemporaneous iGAS isolates for which genomic data were available were included for comparison. Data were analysed in order to determine emm gene sequence type, phylogenetic lineage and genomic clade representation, the presence of known prophage elements and the presence of genes known to confer pathogenicity and resistance to antibiotics. Results 555 isolates were analysed, 303 from patients with SF and 252 from patients with iGAS. Isolates from patients with SF were of multiple distinct emm sequence types and phylogenetic lineages. Prior to data normalisation, emm 3 was the predominant type (accounting for 42.9% of SF isolates, 130/303 95%CI 37.5–48.5; 14.7% higher than the percentage of emm 3 isolates found in the iGAS isolates). Post-normalisation emm types, 4 and 12, were found to be over-represented in patients with SF versus iGAS ( p  < 0.001). A single gene, ssa, was over-represented in isolates from patients with SF. No single phage was found to be over represented in SF vs iGAS. However, a “meta-ssa” phage defined by the presence of :315.2, SPsP6, MGAS10750.3 or HK360ssa, was found to be over represented. The HKU360.vir phage was not detected yet the HKU360.ssa phage was present in 43/63 emm 12 isolates but not found to be over-represented in isolates from patients with SF. Conclusions There is no evidence that the increased number of SF cases was a strain-specific or known mobile element specific phenomenon, as the increase in SF cases was associated with multiple lineages of GAS.