Effects of Ascent to High Altitude on Human Antimycobacterial Immunity

Backgroun

Carbon on the Northwest European Shelf: Contemporary Budget and Future Influences

A carbon budget for the northwest European continental shelf seas (NWES) was synthesized using available estimates for coastal, pelagic and benthic carbon stocks and flows. Key uncertainties were identified and the effect of future impacts on the carbon budget were assessed. The water of the shelf seas contains between 210 and 230 Tmol of carbon and absorbs between 1.3 and 3.3 Tmol from the atmosphere annually. Off-shelf transport and burial in the sediments account for 60–100 and 0–40% of carbon outputs from the NWES, respectively. Both of these fluxes remain poorly constrained by observations and resolving their magnitudes and relative importance is a key research priority. Pelagic and benthic carbon stocks are dominated by inorganic carbon. Shelf sediments contain the largest stock of carbon, with between 520 and 1600 Tmol stored in the top 0.1 m of the sea bed. Coastal habitats such as salt marshes and mud flats contain large amounts of carbon per unit area but their total carbon stocks are small compared to pelagic and benthic stocks due to their smaller spatial extent. The large pelagic stock of carbon will continue to increase due to the rising concentration of atmospheric CO2, with associated pH decrease. Pelagic carbon stocks and flows are also likely to be significantly affected by increasing acidity and temperature, and circulation changes but the net impact is uncertain. Benthic carbon stocks will be affected by increasing temperature and acidity, and decreasing oxygen concentrations, although the net impact of these interrelated changes on carbon stocks is uncertain and a major knowledge gap. The impact of bottom trawling on benthic carbon stocks is unique amongst the impacts we consider in that it is widespread and also directly manageable, although its net effect on the carbon budget is uncertain. Coastal habitats are vulnerable to sea level rise and are strongly impacted by management decisions. Local, national and regional actions have the potential to protect or enhance carbon storage, but ultimately global governance, via controls on emissions, has the greatest potential to influence the long-term fate of carbon stocks in the northwestern European continental shelf

Multiple introductions and human-aided dispersal of the UK’s most widespread non-native amphibian

The alpine newt Ichthyosaura alpestris has achieved a widespread distribution as a non-native (alien) species in Britain since its initial introduction over a century ago, but the patterns of its release and subsequent dispersal have never yet been collectively analysed. We employed a multi-disciplinary combination of methods, using geographic profiling to estimate the likely number and locations of introductions, and mitochondrial DNA polymorphisms to investigate the likely geographic source of primary introductions, including the potential role of the pet trade. In parallel we used population genetic analysis and coalescence-based modelling to infer the demographics and directionality of dispersal from founding populations. Our results show that alpine newts have been released at multiple sites. We found a close resemblance between patterns of mtDNA haplotypes in the pet trade and those of established alpine newt populations, suggesting a relationship between trade, releases, and dispersal. Results from demographic modelling using Approximate Bayesian Computation are also consistent with multiple independent introductions with limited local dispersal, and additionally suggest that releases may occur from intermediate sources, such as captive populations. Our results support the hypothesis that deliberate human activity is largely responsible for both introductions of alpine newts into the UK and their wider dispersal post-introduction. The likely involvement of the international pet trade highlights the risk that ongoing releases of I. alpestris may expose native species to pathogens, whether pre-existing or novel

Bayesian reconstruction of SARS-CoV-2 transmissions highlights substantial proportion of negative serial intervals

BACKGROUND: The serial interval is a key epidemiological measure that quantifies the time between the onset of symptoms in an infector-infectee pair. It indicates how quickly new generations of cases appear, thus informing on the speed of an epidemic. Estimating the serial interval requires to identify pairs of infectors and infectees. Yet, most studies fail to assess the direction of transmission between cases and assume that the order of infections - and thus transmissions - strictly follows the order of symptom onsets, thereby imposing serial intervals to be positive. Because of the long and highly variable incubation period of SARS-CoV-2, this may not always be true (i.e an infectee may show symptoms before their infector) and negative serial intervals may occur. This study aims to estimate the serial interval of different SARS-CoV-2 variants whilst accounting for negative serial intervals. METHODS: This analysis included 5 842 symptomatic individuals with confirmed SARS-CoV-2 infection amongst 2 579 households from September 2020 to August 2022 across England & Wales. We used a Bayesian framework to infer who infected whom by exploring all transmission trees compatible with the observed dates of symptoms, based on a wide range of incubation period and generation time distributions compatible with estimates reported in the literature. Serial intervals were derived from the reconstructed transmission pairs, stratified by variants. RESULTS: We estimated that 22% (95% credible interval (CrI) 8-32%) of serial interval values are negative across all VOC. The mean serial interval was shortest for Omicron BA5 (2.02 days, 1.26-2.84) and longest for Alpha (3.37 days, 2.52-4.04). CONCLUSIONS: This study highlights the large proportion of negative serial intervals across SARS-CoV-2 variants. Because the serial interval is widely used to estimate transmissibility and forecast cases, these results may have critical implications for epidemic control

Enhancer evolution across 20 mammalian species.

The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution.We thank Stephen Watt, Frances Connor, the CRUK-CI Genomics and Bioinformatics cores, Biological Resources Unit (Matthew Clayton), Margaret Brown (West Yorkshire bat hospital), Julie E. Horvath (North Carolina Central University), and Chris Dillingham (University of Cardiff) for technical assistance; Matthieu Muffato for assistance with whole-genome alignments; Claudia Kutter, Gordon Brown, Christine Feig, and Christina Ernst for useful comments and discussions, and the EBI systems team for management of computational resources. This research was supported by Cancer Research UK (D.V., D.T.O.), the European Molecular Biology Laboratory (C.B., P.F.), the Wellcome Trust (WT095908) (P.F.) and (WT098051) (P.F., D.T.O.), the European Research Council, EMBO Young Investigator Programme (D.T.O.), the National Science Foundation (0744979) (T.J.P.), NIH (P40 OD010965, R01 OD010980, R37 MH060233) (A.J.J.) and MRC (U117588498) (J.M.A.T.). Cetacean samples were collected by the UK Cetacean Strandings Investigation Programme, funded by Defra and the Governments of Scotland and Wales.This is the final version. It originally appeared at http://www.sciencedirect.com/science/article/pii/S0092867415000070

T-CaST: an implementation theory comparison and selection tool

Abstract Background Theories, models, and frameworks (TMF) are foundational for generalizing implementation efforts and research findings. However, TMF and the criteria used to select them are not often described in published articles, perhaps due in part to the challenge of selecting from among the many TMF that exist in the field. The objective of this international study was to develop a user-friendly tool to help scientists and practitioners select appropriate TMF to guide their implementation projects. Methods Implementation scientists across the USA, the UK, and Canada identified and rated conceptually distinct categories of criteria in a concept mapping exercise. We then used the concept mapping results to develop a tool to help users select appropriate TMF for their projects. We assessed the tool’s usefulness through expert consensus and cognitive and semi-structured interviews with implementation scientists. Results Thirty-seven implementation scientists (19 researchers and 18 practitioners) identified four criteria domains: usability, testability, applicability, and familiarity. We then developed a prototype of the tool that included a list of 25 criteria organized by domain, definitions of the criteria, and a case example illustrating an application of the tool. Results of cognitive and semi-structured interviews highlighted the need for the tool to (1) be as succinct as possible; (2) have separate versions to meet the unique needs of researchers versus practitioners; (3) include easily understood terms; (4) include an introduction that clearly describes the tool’s purpose and benefits; (5) provide space for noting project information, comparing and scoring TMF, and accommodating contributions from multiple team members; and (6) include more case examples illustrating its application. Interview participants agreed that the tool (1) offered them a way to select from among candidate TMF, (2) helped them be explicit about the criteria that they used to select a TMF, and (3) enabled them to compare, select from among, and/or consider the usefulness of combining multiple TMF. These revisions resulted in the Theory Comparison and Selection Tool (T-CaST), a paper and web-enabled tool that includes 16 specific criteria that can be used to consider and justify the selection of TMF for a given project. Criteria are organized within four categories: applicability, usability, testability, and acceptability. Conclusions T-CaST is a user-friendly tool to help scientists and practitioners select appropriate TMF to guide implementation projects. Additionally, T-CaST has the potential to promote transparent reporting of criteria used to select TMF within and beyond the field of implementation science

Creating testable questions in practical conservation: a process and 100 questions

It is now clear that the routine embedding of experiments into conservation practice is essential for creating reasonably comprehensive evidence of the effectiveness of actions. However, an important barrier is the stage of identifying testable questions that are both useful but also realistic to carry out without a major research project. We identified approaches for generating such suitable questions. A team of 24 participants crowdsourced suggestions, resulting in a list of a hundred possible tests of actions.Additional co-authors: Roger Mitchell, William H. Morgan, Roy Mosley, Silviu O. Petrovan, Kit Prendergast, Euan G. Ritchie, Hugh Raven, Rebecca K. Smith & Ann Thornto

Creating testable questions in practical conservation: a process and 100 questions

It is now clear that the routine embedding of experiments into conservation practice is essential for creating reasonably comprehensive evidence of the effectiveness of actions. However, an important barrier is the stage of identifying testable questions that are both useful but also realistic to carry out without a major research project. We identified approaches for generating such suitable questions. A team of 24 participants crowdsourced suggestions, resulting in a list of a hundred possible tests of actions

Carbon on the Northwest European Shelf: Contemporary Budget and Future Influences

© Copyright © 2020 Legge, Johnson, Hicks, Jickells, Diesing, Aldridge, Andrews, Artioli, Bakker, Burrows, Carr, Cripps, Felgate, Fernand, Greenwood, Hartman, Kröger, Lessin, Mahaffey, Mayor, Parker, Queirós, Shutler, Silva, Stahl, Tinker, Underwood, Van Der Molen, Wakelin, Weston and Williamson. A carbon budget for the northwest European continental shelf seas (NWES) was synthesized using available estimates for coastal, pelagic and benthic carbon stocks and flows. Key uncertainties were identified and the effect of future impacts on the carbon budget were assessed. The water of the shelf seas contains between 210 and 230 Tmol of carbon and absorbs between 1.3 and 3.3 Tmol from the atmosphere annually. Off-shelf transport and burial in the sediments account for 60–100 and 0–40% of carbon outputs from the NWES, respectively. Both of these fluxes remain poorly constrained by observations and resolving their magnitudes and relative importance is a key research priority. Pelagic and benthic carbon stocks are dominated by inorganic carbon. Shelf sediments contain the largest stock of carbon, with between 520 and 1600 Tmol stored in the top 0.1 m of the sea bed. Coastal habitats such as salt marshes and mud flats contain large amounts of carbon per unit area but their total carbon stocks are small compared to pelagic and benthic stocks due to their smaller spatial extent. The large pelagic stock of carbon will continue to increase due to the rising concentration of atmospheric CO2, with associated pH decrease. Pelagic carbon stocks and flows are also likely to be significantly affected by increasing acidity and temperature, and circulation changes but the net impact is uncertain. Benthic carbon stocks will be affected by increasing temperature and acidity, and decreasing oxygen concentrations, although the net impact of these interrelated changes on carbon stocks is uncertain and a major knowledge gap. The impact of bottom trawling on benthic carbon stocks is unique amongst the impacts we consider in that it is widespread and also directly manageable, although its net effect on the carbon budget is uncertain. Coastal habitats are vulnerable to sea level rise and are strongly impacted by management decisions. Local, national and regional actions have the potential to protect or enhance carbon storage, but ultimately global governance, via controls on emissions, has the greatest potential to influence the long-term fate of carbon stocks in the northwestern European continental shelf