Implementing a multisite shared haemodialysis care programme

Adults receiving centre-based haemodialysis (HD) have low levels of patient activation which are associated with poorer outcomes. Shared haemodialysis care (SHC) describes an intervention whereby individuals are supported to undertake elements of their treatment to improve their activation levels and promote better self-care. This project aimed to increase the proportion of those performing SHC in seven HD centres within the Oxford Kidney Unit's catchment area. Sequential Plan-Do-Study-Act (PDSA) cycles effected change first in two central HD centres, in cycles 1 and 2, before rolling out to five satellite HD centres, in cycles 3 and 4. Cycle 1 explored and transformed staff perceptions regarding SHC using a questionnaire and teaching sessions while in cycle 2, staff partnered with patients to develop leaflets and noticeboards to improve awareness and participation. These interventions were then rolled out to the remaining HD centres in PDSA cycles 3 and 4. Other interventions included: Enrolling staff and patients in virtual training courses; designating SHC 'Champions'; engagement with a national SHC forum; and changes to the electronic patient record to enable the monitoring of patient SHC opportunity and to promote sustainable change. Outcome measurement data on the number of patients performing SHC and the number at different defined stages of SHC competency were captured monthly. In April 2022, only 4% (19/483) of those receiving centre-based HD performed any aspect of SHC. By the end of the project in December 2023, this had increased to 43% (220/511). There was a significant and sustained growth in the stage of patient SHC competency as well as the number of patients performing SHC in each HD centre. The project demonstrated that it is possible to implement, scale-up and maintain a multisite SHC programme even with little baseline staff and patient SHC experience

The effect of flooding and drainage duration on the release of trace elements from floodplain soils

Floodplains downstream of urban catchments are sinks for potentially toxic trace elements. An intensification of the hydrological cycle and changing land use will result in floodplains becoming inundated for longer durations in the future. We collected intact soil cores from a floodplain meadow downstream of an urban catchment and subjected them to an inundation/drainage cycle in the laboratory to investigate the effect of flood duration on trace element concentrations in the soil porewater. The porewater concentrations of Ni, Cr, and Zn increased, whereas Cu and Pb decreased with flood duration. All the Cr present in porewaters was identified as Cr(III). Copper concentrations increased after drainage but Pb mobility remained suppressed. Both pH and dissolved organic carbon (DOC) increased with flood duration but were lower in treatments that were drained for the longest duration (which were also the treatments flooded for the shortest duration). The porewater concentrations of Cr and Ni decreased after drainage to levels below those observed before inundation, mirroring the DOC concentrations. We concluded that the duration of floodplain inundation does have an influence on the environmental fate of trace elements but that flooding does not influence all trace elements in the same way. The implications of an intensification of the hydrological cycle over the coming decades are that floodplains may become a source of some trace elements to aquatic and terrestrial ecosystems. Environ Toxicol Chem 2020;39:2124–2135

Dual stresses of flooding and agricultural land use reduce earthworm populations more than the individual stressors

Global climate change is leading to a significant increase in flooding events in many countries. Current practices to prevent damage to downstream urban areas include allowing the flooding of upstream agricultural land. Earthworms are ecosystem engineers, but their abundances in arable land are already reduced due to pressure from farming practices. If flooding increases on agricultural land, it is important to understand how earthworms will respond to the dual stresses of flooding and agricultural land use. The earthworm populations under three land uses (pasture, field margin, and crops), across two UK fields, were sampled seasonally over an 18-month period in areas of the fields which flood frequently and areas which flood only rarely. Earthworm abundance in the crop and pasture soils and total earthworm biomass in the crop soils was significantly lower in the frequently flooded areas than in the rarely flooded areas. The relative percentage difference in the populations between the rarely and frequently flooded areas was greater in the crop soils (−59.18% abundance, −63.49% biomass) than the pasture soils (−13.39% abundance, −9.66% biomass). In the margin soils, earthworm abundance was significantly greater in the frequently flooded areas (+140.56%), likely due to higher soil organic matter content and lower bulk density resulting in soil conditions more amenable to earthworms. The findings of this study show that earthworm populations already stressed by the activities associated with arable land use are more susceptible to flooding than populations in pasture fields, suggesting that arable earthworm populations are likely to be increasingly at risk with increased flooding

Analysis of the African coelacanth genome sheds light on tetrapod evolution

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

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

Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature0315

Impact of fluvial flooding on potentially toxic element mobility in floodplain soil

Global climate change is associated with significant changes to short-term weather extremes as well as long-term weather characteristics in different regions. Whilst the magnitude of climate changes are extremely uncertain, it is likely that summers will become warmer and drier, and there will be an increase in the intensity of rainfall events. These intense rainfall events will lead to an increased number of flooding events that remain for longer periods of time, and the occasional inundation of land that has rarely been flooded in the past. There is the possibility that increased flooding intensity and frequency will influence the soil properties, which in turn may affect the behaviour and mobilisation of potentially toxic elements (PTEs) in floodplain soils. It likely that many floodplains downstream of urban catchments, particularly those catchments with a history of industrial development, may harbour a legacy of contaminants that have been deposited with floodplain sediments. To investigate the impact of fluvial flooding on PTE mobility in floodplain soils, I used the Loddon Meadow floodplain site; situated adjacent to the River Loddon in the Southeast of England, as a model floodplain, typical of a lowland floodplain downstream of an urban catchment. Preliminary work characterised the floodplain topography using geospatial techniques and compared elevation with the spatial distribution of soil PTEs concentrations. The topography of the floodplain was found to influence the deposition of some PTEs (e.g. Cr, Cu, Ni and Zn), providing strong evidence that the source of these PTEs to this floodplain site originated from point source or diffuse pollution upstream in the urban catchment. The novel combination of geospatial mapping of elevation and geochemical analyses could be adopted as a method for determining the source of PTEs to other study sites. Analysing soil pore water chemistry provides the more useful measurement of the mobile fraction of PTEs, rather than the total concentration bound to the solid fraction. There are a number of methods for extracting pore water from soil samples; we compared an example of an in-situ method (RhizonTM sampler) with an example of an ex-situ method (centrifugation). There were no significant differences found in the pore water chemistry, despite the centrifugation exerting a pressure on the soil sample orders of magnitude higher than the RhizonTM sampler. We found, however, that in terms of useability through a range of soil moistures and consistency of sample volume extracted, the centrifuge was the preferred method for this particular study. We highlight examples where the opposite conclusion might be reached. Laboratory mesocosm studies have reported increased PTE mobilisation with artificial flooding events. However, it can be difficult to extrapolate these finding due to the controlled conditions of the laboratory set-up (e.g. room temperatures are often higher than found in the field). We found that there was a need for on-site experiments that consider the effects of flooding using real-time field observations. We therefore took a field-based approach; extracting soil pore waters, by centrifugation, from the Loddon Meadow floodplain pre-flood, during a flood and post-flood. We found that the flooding event did not influence the mobility of all of the PTEs in the same way. However, we found concentrations of Cd, Cu and Cr significantly decreased post-flood compared to pre-flood. The dominant process identified to explain this decrease was precipitation with sulphides, which occurred during the flood and subsequently resulted in the significant decrease in concentrations post-flood. A slight increase in pH may have aided adsorption processes onto organic matter and clay minerals. We also found a decrease in dissolved organic matter in solution and this would have reduced the capability of the pore water to complex PTEs in solution. It is possible that the decreased concentrations found were a result of dilution, due to the increased water volume from the river and ground water. When analysed, the river and ground water had considerably lower concentrations of PTEs than the soil pore waters. The impact of a flooding event on PTEs mobility is the combination of multiple processes. So, while we observed some processes increasing the concentrations of PTEs; for example, the reductive dissolution of Mn oxides, predominantly in the lower elevation areas of the floodplain. The overall net effect of the flooding event was a decrease in PTE concentrations, because processes like sulphide precipitation were dominant. There were no significant increases in PTEs mobility due to the flooding event and as such, no evidence to support the idea that floodplains become a source of PTEs. This is contrary to the evidence from laboratory studies, that found there is mobilisation of PTEs due to flooding. This study highlights the importance of understanding the dominant processes that drive the mobility of individual PTEs on specific floodplains, so that site-specific predictions can be made on the impact of future flooding on the mobilisation of legacy contaminants. Further field-based monitoring; collecting data pre-flood, during the flood and post-flood, from varying soil types and composition (e.g. clay, sand, silt, peat and loam) is required to support future modelling exercises. This would improve our capability to predict the impact of increased intensity and duration of flooding on soil porewater chemistry and PTE mobility

Impact of fluvial flooding on potentially toxic element mobility in floodplain soils 

&amp;lt;p&amp;gt;Climate projections suggest that rainfall events will become more frequent and intense, which may lead to more widespread flooding. Floodplains can be used to help reduce the magnitude of floods downstream by storing excess flood water, thus making them useful for flood risk management. This means that floodplains are subjected to repeated drying and rewetting, which has implications for biogeochemical cycling of chemical elements in floodplain soils.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Floodplains have been considered a sink for contaminants in urban catchments, where high river flows transport contaminated sediments downstream and deposit them onto the floodplain topsoil. With increasing flooding frequency and duration, floodplains may become sources of legacy pollution through desorption of contaminants into soil porewater or resuspension of particulate matter into the overlying floodwater. Therefore, flooding could re-mobilise potentially toxic elements (PTEs) such as Cadmium (Cd), Copper (Cu), Chromium (Cr), Nickel (Ni), and Lead (Pb) that are present in the floodplain soil as a result of historic deposition. Mobilising PTEs in floodplain soils may cause adverse ecological impacts for soil microorganisms, plants, and both terrestrial and aquatic fauna.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;The mobility of PTEs from the floodplain soil can increase or decrease due to the net effect of five key processes that influence dispersion and accumulation; 1) soil redox potential for which decreases &amp;amp;#160;can directly alter the speciation, and hence mobility, of redox sensitive PTEs (e.g. As and Cr), 2) soil pH for which an increase usually reduces the mobility of metal cations (e.g. Cd&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt;, Cu&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt;, Ni&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt;, Pb&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt;), 3) dissolved organic matter which can mobilise PTEs were strongly bound to soil particles, 4) iron (Fe) and manganese (Mn) hydroxides undergo reductive dissolution, releasing adsorbed and co-precipitated PTEs, and 5) reduction of sulphate which immobilises PTEs due to precipitation of metal sulphides.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;We took a field-based approach; extracting soil pore waters from a floodplain downstream of a typical urban catchment in southeast England before, during and after a flooding event. During the flood, there was increased mobility of Cd and Pb, and decreased mobility for Cu and Cr, compared to the mobility before flooding. After the flood, Ni mobility increased, whereas the other PTEs had lower mobility than they had prior to the flood. We also measured explanatory variables (e.g. pH, redox, Fe and Mn) that might explain the changes in mobility of PTEs that we found. Reductive dissolution of Mn is a possible mechanism for the increased mobility of Cd and Pb and redox likely played a role in the reduced Cr mobility.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Flooding did not influence the mobility of all PTEs in the same way. The duration of flooding is thought to influence the mobilisation due to the length of time for key processes to take place. It is therefore difficult to predict what PTEs might be mobilised into the environment with any given flooding event, further work is required to identify which soil properties should be measured in order to improve our capability to predict how a flooding event will influence the mobility of individual PTEs in geochemically contrasting floodplain soils.&amp;lt;/p&amp;gt;</jats:p