Developing the repository manager community

This paper describes activities which have taken place within the UK institutional repository (IR) sector focusing on developing a community of practice through the sharing of experiences and best practice. This includes work done by the UK Council of Research Repositories (UKCoRR) and other bodies, together with informal activities, such as sharing the experience of organising Open Access Week events. The paper also considers future work to be undertaken by UKCoRR to continue developing the community

Main-Belt Comet P/2012 T1 (PANSTARRS)

We present initial results from observations and numerical analyses aimed at characterizing main-belt comet P/2012 T1 (PANSTARRS). Optical monitoring observations were made between October 2012 and February 2013 using the University of Hawaii 2.2 m telescope, the Keck I telescope, the Baade and Clay Magellan telescopes, Faulkes Telescope South, the Perkins Telescope at Lowell Observatory, and the Southern Astrophysical Research (SOAR) telescope. The object's intrinsic brightness approximately doubles from the time of its discovery in early October until mid-November and then decreases by ~60% between late December and early February, similar to photometric behavior exhibited by several other main-belt comets and unlike that exhibited by disrupted asteroid (596) Scheila. We also used Keck to conduct spectroscopic searches for CN emission as well as absorption at 0.7 microns that could indicate the presence of hydrated minerals, finding an upper limit CN production rate of QCN<1.5x10^23 mol/s, from which we infer a water production rate of QH2O<5x10^25 mol/s, and no evidence of the presence of hydrated minerals. Numerical simulations indicate that P/2012 T1 is largely dynamically stable for >100 Myr and is unlikely to be a recently implanted interloper from the outer solar system, while a search for potential asteroid family associations reveal that it is dynamically linked to the ~155 Myr-old Lixiaohua asteroid family.Comment: 15 pages, 4 figures, accepted for publication in ApJ Letter

Effect of Pneumococcal Conjugate Vaccines on Pneumococcal Meningitis, England and Wales, July 1, 2000–June 30, 2016

We describe the effects of the 7-valent (PCV7) and 13-valent (PCV13) pneumococcal conjugate vaccines on pneumococcal meningitis in England and Wales during July 1, 2000–June 30, 2016. Overall, 84,473 laboratory-confirmed invasive pneumococcal disease cases, including 4,160 (4.9%) cases with meningitis, occurred. PCV7 implementation in 2006 did not lower overall pneumococcal meningitis incidence because of replacement with non–PCV7-type meningitis incidence. Replacement with PCV13 in 2010, however, led to a 48% reduction in pneumococcal meningitis incidence by 2015–16. The overall case-fatality rate was 17.5%: 10.7% among patients 65 years of age. Serotype 8 was associated with increased odds of death (adjusted odds ratio 2.9, 95% CI 1.8–4.7). In England and Wales, an effect on pneumococcal meningitis was observed only after PCV13 implementation. Further studies are needed to assess pneumococcal meningitis caused by the replacing serotypes

Effect of Pneumococcal Conjugate Vaccination on Serotype-Specific Carriage and Invasive Disease in England: A Cross-Sectional Study

A cross sectional study by Stefan Flasche and coworkers document the serotype replacement of Streptococcus pneumoniae that has occurred in England since the introduction of PCV7 vaccination

Methane emissions from soils: synthesis and analysis of a large UK data set

Nearly 5000 chamber measurements of CH4 flux were collated from 21 sites across the UK, covering a range of soil and vegetation types, to derive a parsimonious model that explains as much of the variability as possible, with the least input requirements. Mean fluxes ranged from -0.3 to 27.4 nmol CH4 m−2 s−1, with small emissions or low rates of net uptake in mineral soils (site means of -0.3 to 0.7 nmol m−2 s−1) and much larger emissions from organic soils (site means of -0.3 to 27.4 nmol m−2 s−1). Less than half of the observed variability in instantaneous fluxes could be explained by independent variables measured. The reasons for this include measurement error, stochastic processes and, probably most importantly, poor correspondence between the independent variables measured and the actual variables influencing the processes underlying methane production, transport and oxidation. When temporal variation was accounted for, and the fluxes averaged at larger spatial scales, simple models explained up to ~75% of the variance in CH4 fluxes. Soil carbon, peat depth, soil moisture and pH together provided the best sub-set of explanatory variables. However, where plant species composition data were available, this provided the highest explanatory power. Linear and non-linear models generally fitted the data equally well, with the exception that soil moisture required a power transformation. To estimate the impact of changes in peatland water table on CH4 emissions in the UK, an emission factor of +0.4 g CH4 m−2 y−1 per cm increase in water table height was derived from the data

Patterns of Gene Flow Define Species of Thermophilic Archaea

A genomic view of speciation in Archaea shows higher rates of gene flow within coexisting microbial species than between them

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK

Following primary SARS-CoV-2 vaccination, whether boosters or breakthrough infections provide greater protection against SARS-CoV-2 infection is incompletely understood. Here we investigated SARS-CoV-2 antibody correlates of protection against new Omicron BA.4/5 (re-)infections and anti-spike IgG antibody trajectories after a third/booster vaccination or breakthrough infection following second vaccination in 154,149 adults ≥18 y from the United Kingdom general population. Higher antibody levels were associated with increased protection against Omicron BA.4/5 infection and breakthrough infections were associated with higher levels of protection at any given antibody level than boosters. Breakthrough infections generated similar antibody levels to boosters, and the subsequent antibody declines were slightly slower than after boosters. Together our findings show breakthrough infection provides longer-lasting protection against further infections than booster vaccinations. Our findings, considered alongside the risks of severe infection and long-term consequences of infection, have important implications for vaccine policy

Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population

SARS-CoV-2 reinfections increased substantially after Omicron variants emerged. Large-scale community-based comparisons across multiple Omicron waves of reinfection characteristics, risk factors, and protection afforded by previous infection and vaccination, are limited. Here we studied ~45,000 reinfections from the UK’s national COVID-19 Infection Survey and quantified the risk of reinfection in multiple waves, including those driven by BA.1, BA.2, BA.4/5, and BQ.1/CH.1.1/XBB.1.5 variants. Reinfections were associated with lower viral load and lower percentages of self-reporting symptoms compared with first infections. Across multiple Omicron waves, estimated protection against reinfection was significantly higher in those previously infected with more recent than earlier variants, even at the same time from previous infection. Estimated protection against Omicron reinfections decreased over time from the most recent infection if this was the previous or penultimate variant (generally within the preceding year). Those 14–180 days after receiving their most recent vaccination had a lower risk of reinfection than those &gt;180 days from their most recent vaccination. Reinfection risk was independently higher in those aged 30–45 years, and with either low or high viral load in their most recent previous infection. Overall, the risk of Omicron reinfection is high, but with lower severity than first infections; both viral evolution and waning immunity are independently associated with reinfection