A vertical representation of soil carbon in the JULES land surface scheme (vn4.3_permafrost) with a focus on permafrost regions

An improved representation of the carbon cycle in permafrost regions will enable more realistic projections of the future climate–carbon system. Currently JULES (the Joint UK Land Environment Simulator) – the land surface model of the UK Earth System Model (UKESM) – uses the standard four-pool RothC soil carbon model. This paper describes a new version of JULES (vn4.3_permafrost) in which the soil vertical dimension is added to the soil carbon model, with a set of four pools in every soil layer. The respiration rate in each soil layer depends on the temperature and moisture conditions in that layer. Cryoturbation/bioturbation processes, which transfer soil carbon between layers, are represented by diffusive mixing. The litter inputs and the soil respiration are both parametrized to decrease with increasing depth. The model now includes a tracer so that selected soil carbon can be labelled and tracked through a simulation. Simulations show an improvement in the large-scale horizontal and vertical distribution of soil carbon over the standard version of JULES (vn4.3). Like the standard version of JULES, the vertically discretized model is still unable to simulate enough soil carbon in the tundra regions. This is in part because JULES underestimates the plant productivity over the tundra, but also because not all of the processes relevant for the accumulation of permafrost carbon, such as peat development, are included in the model. In comparison with the standard model, the vertically discretized model shows a delay in the onset of soil respiration in the spring, resulting in an increased net uptake of carbon during this time. In order to provide a more suitable representation of permafrost carbon for quantifying the permafrost carbon feedback within UKESM, the deep soil carbon in the permafrost region (below 1 m) was initialized using the observed soil carbon. There is now a slight drift in the soil carbon ( <  0.018 % decade−1), but the change in simulated soil carbon over the 20th century, when there is little climate change, is comparable to the original vertically discretized model and significantly larger than the drift

An observation-based constraint on permafrost loss as a function of global warming

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordPermafrost, which covers 15 million km 2 of the land surface, is one of the components of the Earth system that is most sensitive to warming. Loss of permafrost would radically change high-latitude hydrology and biogeochemical cycling, and could therefore provide very significant feedbacks on climate change. The latest climate models all predict warming of high-latitude soils and thus thawing of permafrost under future climate change, but with widely varying magnitudes of permafrost thaw. Here we show that in each of the models, their present-day spatial distribution of permafrost and air temperature can be used to infer the sensitivity of permafrost to future global warming. Using the same approach for the observed permafrost distribution and air temperature, we estimate a sensitivity of permafrost area loss to global mean warming at stabilization of million km 2 °C â '1 (1σ confidence), which is around 20% higher than previous studies. Our method facilitates an assessment for COP21 climate change targets: if the climate is stabilized at 2 °C above pre-industrial levels, we estimate that the permafrost area would eventually be reduced by over 40%. Stabilizing at 1.5 °C rather than 2 °C would save approximately 2 million km 2 of permafrost.European Union Seventh Framework ProgrammeNatural Environment Research Council (NERC)Swedish Research CouncilResearch Council of NorwayUK DECC/Defra Met Office HadleyEuropean Unio

Germinal Center B Cells Regulate Their Capability to Present Antigen by Modulation of HLA-DO

Peptide acquisition by MHC class II molecules is catalyzed by HLA-DM (DM). In B cells, HLA-DO (DO) inhibits or modifies the peptide exchange activity of DM. We show here that DO protein levels are modulated during B cell differentiation. Remarkably, germinal center (GC) B cells, which have low levels of DO relative to naive and memory B cells, are shown to have enhanced antigen presentation capabilities. DM protein levels also were somewhat reduced in GC B cells; however, the ratio of DM to DO in GC B cells was substantially increased, resulting in more free DM in GC B cells. We conclude that modulation of DM and DO in distinct stages of B cell differentiation represents a mechanism by which B cells regulate their capacity to function as antigen-presenting cells. Efficient antigen presentation in GC B cells would promote GC B cell–T cell interactions that are essential for B cells to survive positive selection in the GC

Simulated responses of soil carbon to climate change in CMIP6 Earth system models: the role of false priming

This is the final version. Available from Copernicus Publications / European Geosciences Union via the DOI in this record. The CMIP data analysed during this study are available online: CMIP6 (https://esgf-node.llnl.gov/search/cmip6/, last access: 8 April 2022) and CMIP5 (https://esgf-node.llnl.gov/search/cmip5/, last access: 12 April 2022).Code is available on GitHub (https://github.com/rebeccamayvarney/CMIP6_dCs, last access: 28 July 2023).Reliable estimates of soil carbon change are required to determine the carbon budgets consistent with the Paris Agreement climate targets. This study evaluates projections of soil carbon during the 21st century in Coupled Model Intercomparison Project Phase 6 (CMIP6) Earth system models (ESMs) under a range of atmospheric composition scenarios. In general, we find a reduced spread of changes in global soil carbon (ΔCs) in CMIP6 compared to the previous CMIP5 model generation. However, similar reductions were not seen in the derived contributions to ΔCs due to both increases in plant net primary productivity (NPP, named ΔCs,NPP) and reductions in the effective soil carbon turnover time (τs, named ΔCs,τ). Instead, we find a strong relationship across the CMIP6 models between these NPP and τs components of ΔCs, with more positive values of ΔCs,NPP being correlated with more negative values of ΔCs,τ. We show that the concept of “false priming” is likely to be contributing to this emergent relationship, which leads to a decrease in the effective soil carbon turnover time as a direct result of NPP increase and occurs when the rate of increase in NPP is relatively fast compared to the slower timescales of a multi-pool soil carbon model. This finding suggests that the structure of soil carbon models within ESMs in CMIP6 has likely contributed towards the reduction in the overall model spread in future soil carbon projections since CMIP5.European Union’s Horizon 2020European Union’s Horizon 202

Experiences of in-patient mental health services: systematic review

Background In-patients in crisis report poor experiences of mental healthcare not conducive to recovery. Concerns include coercion by staff, fear of assault from other patients, lack of therapeutic opportunities and limited support. There is little high-quality evidence on what is important to patients to inform recovery-focused care.Aims To conduct a systematic review of published literature, identifying key themes for improving experiences of in-patient mental healthcare.Method A systematic search of online databases (MEDLINE, PsycINFO and CINAHL) for primary research published between January 2000 and January 2016. All study designs from all countries were eligible. A qualitative analysis was undertaken and study quality was appraised. A patient and public reference group contributed to the review.Results Studies (72) from 16 countries found four dimensions were consistently related to significantly influencing in-patients' experiences of crisis and recovery-focused care: the importance of high-quality relationships; averting negative experiences of coercion; a healthy, safe and enabling physical and social environment; and authentic experiences of patient-centred care. Critical elements for patients were trust, respect, safe wards, information and explanation about clinical decisions, therapeutic activities, and family inclusion in care.Conclusions A number of experiences hinder recovery-focused care and must be addressed with the involvement of staff to provide high-quality in-patient services. Future evaluations of service quality and development of practice guidance should embed these four dimensions.Declaration of interest K.B. is editor of British Journal of Psychiatry and leads a national programme (Synergi Collaborative Centre) on patient experiences driving change in services and inequalities

The effect of extra dimensions on gravity wave bursts from cosmic string cusps

We explore the kinematical effect of having extra dimensions on the gravity wave emission from cosmic strings. Additional dimensions both round off cusps, and reduce the probability of their formation. We recompute the gravity wave burst, taking into account these two factors, and find a potentially significant damping on the gravity waves of the strings.Comment: 33 pages, 8 figures, published versio

Large stocks of peatland carbon and nitrogen are vulnerable to permafrost thaw

This is the final version. Available on open access from the National Academy of Sciences via the DOI in this recordData Availability. The results and peat core data are summarized in Datasets S1–S6. Maps of predicted peatland extent, peat depth, and peat C and N storage (10-km pixels) are archived and freely available for download at https://bolin.su.se/data/hugelius-2020Northern peatlands have accumulated large stocks of organic carbon (C) and nitrogen (N), but their spatial distribution and vulnerability to climate warming remain uncertain. Here, we used machine-learning techniques with extensive peat core data (n > 7,000) to create observation-based maps of northern peatland C and N stocks, and to assess their response to warming and permafrost thaw. We estimate that northern peatlands cover 3.7 ± 0.5 million km2 and store 415 ± 150 Pg C and 10 ± 7 Pg N. Nearly half of the peatland area and peat C stocks are permafrost affected. Using modeled global warming stabilization scenarios (from 1.5 to 6 °C warming), we project that the current sink of atmospheric C (0.10 ± 0.02 Pg C⋅y-1) in northern peatlands will shift to a C source as 0.8 to 1.9 million km2 of permafrost-affected peatlands thaw. The projected thaw would cause peatland greenhouse gas emissions equal to ∼1% of anthropogenic radiative forcing in this century. The main forcing is from methane emissions (0.7 to 3 Pg cumulative CH4-C) with smaller carbon dioxide forcing (1 to 2 Pg CO2-C) and minor nitrous oxide losses. We project that initial CO2-C losses reverse after ∼200 y, as warming strengthens peatland C-sinks. We project substantial, but highly uncertain, additional losses of peat into fluvial systems of 10 to 30 Pg C and 0.4 to 0.9 Pg N. The combined gaseous and fluvial peatland C loss estimated here adds 30 to 50% onto previous estimates of permafrost-thaw C losses, with southern permafrost regions being the most vulnerable.Swedish Research CouncilEuropean UnionEuropean Union Horizon 2020Gordon and Betty and Gordon Moore FoundationNatural Environment Research Council (NERC)National Science FoundationNational Natural Science Foundation of Chin

An improved representation of physical permafrost dynamics in the JULES land-surface model

PublishedJournal Article© Author(s) 2015. It is important to correctly simulate permafrost in global climate models, since the stored carbon represents the source of a potentially important climate feedback. This carbon feedback depends on the physical state of the permafrost. We have therefore included improved physical permafrost processes in JULES (Joint UK Land Environment Simulator), which is the land-surface scheme used in the Hadley Centre climate models. The thermal and hydraulic properties of the soil were modified to account for the presence of organic matter, and the insulating effects of a surface layer of moss were added, allowing for fractional moss cover. These processes are particularly relevant in permafrost zones. We also simulate a higher-resolution soil column and deeper soil, and include an additional thermal column at the base of the soil to represent bedrock. In addition, the snow scheme was improved to allow it to run with arbitrarily thin layers. Point-site simulations at Samoylov Island, Siberia, show that the model is now able to simulate soil temperatures and thaw depth much closer to the observations. The root mean square error for the near-surface soil temperatures reduces by approximately 30%, and the active layer thickness is reduced from being over 1 m too deep to within 0.1 m of the observed active layer thickness. All of the model improvements contribute to improving the simulations, with organic matter having the single greatest impact. A new method is used to estimate active layer depth more accurately using the fraction of unfrozen water. Soil hydrology and snow are investigated further by holding the soil moisture fixed and adjusting the parameters to make the soil moisture and snow density match better with observations. The root mean square error in near-surface soil temperatures is reduced by a further 20% as a result

Green Plants in the Red: A Baseline Global Assessment for the IUCN Sampled Red List Index for Plants

Plants provide fundamental support systems for life on Earth and are the basis for all terrestrial ecosystems; a decline in plant diversity will be detrimental to all other groups of organisms including humans. Decline in plant diversity has been hard to quantify, due to the huge numbers of known and yet to be discovered species and the lack of an adequate baseline assessment of extinction risk against which to track changes. The biodiversity of many remote parts of the world remains poorly known, and the rate of new assessments of extinction risk for individual plant species approximates the rate at which new plant species are described. Thus the question ‘How threatened are plants?’ is still very difficult to answer accurately. While completing assessments for each species of plant remains a distant prospect, by assessing a randomly selected sample of species the Sampled Red List Index for Plants gives, for the first time, an accurate view of how threatened plants are across the world. It represents the first key phase of ongoing efforts to monitor the status of the world’s plants. More than 20% of plant species assessed are threatened with extinction, and the habitat with the most threatened species is overwhelmingly tropical rain forest, where the greatest threat to plants is anthropogenic habitat conversion, for arable and livestock agriculture, and harvesting of natural resources. Gymnosperms (e.g. conifers and cycads) are the most threatened group, while a third of plant species included in this study have yet to receive an assessment or are so poorly known that we cannot yet ascertain whether they are threatened or not. This study provides a baseline assessment from which trends in the status of plant biodiversity can be measured and periodically reassessed