Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

An analysis of fish community responses to coral mining in the Maldives

Coral mining takes place on shallow reef flats at a number of localities in the Maldives, but not on the adjacent deeper reef slopes. A semi-quantitative census method for fish species abundance and biomass is described. Fish community structure is compared on mined and non-mined reef flats and their adjacent slopes using a variety of univariate, graphical/distributional and multivariate statistical techniques. In general, univariate and graphical distributional methods do not indicate significant differences between mined and non-mined localities with respect to the relative abundances and biomasses of species. Multivariate methods (both classification and ordination), however, indicate very clear-cut effects of mining on the reef flats, and also significant effects on reef slopes adjacent to mined flats. The effect was equally clear using non-quantitative (presence/absence) data. The fish species mainly responsible for the differences between mined and non-mined localities are identified, and the differences are explained in terms of the feeding biology of these species

Extinction vulnerability in marine populations

Human impacts on the world's oceans have been substantial, leading to concerns about the extinction of marine taxa. We have compiled 133 local, regional and global extinctions of marine populations. There is typically a 53-year lag between the last sighting of an organism and the reported date of the extinction at whatever scale this has occurred. Most disappearances (80%) were detected using indirect historical comparative methods, which suggests that marine extinctions may have been underestimated because of low-detection power. Exploitation caused most marine losses at various scales (55%), followed closely by habitat loss (37%), while the remainder were linked to invasive species, climate change, pollution and disease. Several perceptions concerning the vulnerability of marine organisms appear to be too general and insufficiently conservative. Marine species cannot be considered less vulnerable on the basis of biological attributes such as high fecundity or large-scale dispersal characteristics. For commercially exploited species, it is often argued that economic extinction of exploited populations will occur before biological extinction, but this is not the case for non-target species caught in multispecies fisheries or species with high commercial value, especially if this value increases as species become rare. The perceived high potential for recovery, high variability and low extinction vulnerability of fish populations have been invoked to avoid listing commercial species of fishes under international threat criteria. However, we need to learn more about recovery, which may be hampered by negative population growth at small population sizes (Allee effect or depensation) or ecosystem shifts, as well as about spatial dynamics and connectivity of subpopulations before we can truly understand the nature of responses to severe depletions. The evidence suggests that fish populations do not fluctuate more than those of mammals, birds and butterflies, and that fishes may exhibit vulnerability similar to mammals, birds and butterflies. There is an urgent need for improved methods of detecting marine extinctions at various spatial scales, and for predicting the vulnerability of species

Critical care usage after major gastrointestinal and liver surgery: a prospective, multicentre observational study

Background: Patient selection for critical care admission must balance patient safety with optimal resource allocation. This study aimed to determine the relationship between critical care admission, and postoperative mortality after abdominal surgery. Methods: This prespecified secondary analysis of a multicentre, prospective, observational study included consecutive patients enrolled in the DISCOVER study from UK and Republic of Ireland undergoing major gastrointestinal and liver surgery between October and December 2014. The primary outcome was 30-day mortality. Multivariate logistic regression was used to explore associations between critical care admission (planned and unplanned) and mortality, and inter-centre variation in critical care admission after emergency laparotomy. Results: Of 4529 patients included, 37.8% (n=1713) underwent planned critical care admissions from theatre. Some 3.1% (n=86/2816) admitted to ward-level care subsequently underwent unplanned critical care admission. Overall 30-day mortality was 2.9% (n=133/4519), and the risk-adjusted association between 30-day mortality and critical care admission was higher in unplanned [odds ratio (OR): 8.65, 95% confidence interval (CI): 3.51–19.97) than planned admissions (OR: 2.32, 95% CI: 1.43–3.85). Some 26.7% of patients (n=1210/4529) underwent emergency laparotomies. After adjustment, 49.3% (95% CI: 46.8–51.9%, P<0.001) were predicted to have planned critical care admissions, with 7% (n=10/145) of centres outside the 95% CI. Conclusions: After risk adjustment, no 30-day survival benefit was identified for either planned or unplanned postoperative admissions to critical care within this cohort. This likely represents appropriate admission of the highest-risk patients. Planned admissions in selected, intermediate-risk patients may present a strategy to mitigate the risk of unplanned admission. Substantial inter-centre variation exists in planned critical care admissions after emergency laparotomies

Colorectal Endoscopic Stenting Trial (CReST) for obstructing left-sided colorectal cancer: randomized clinical trial

Background Colorectal cancer often presents with obstruction needing urgent, potentially life-saving decompression. The comparative efficacy and safety of endoluminal stenting versus emergency surgery as initial treatment for such patients is uncertain. Methods Patients with left-sided colonic obstruction and radiological features of carcinoma were randomized to endoluminal stenting using a combined endoscopic/fluoroscopic technique followed by elective surgery 1–4 weeks later, or surgical decompression with or without tumour resection. Treatment allocation was via a central randomization service using a minimization procedure stratified by curative intent, primary tumour site, and severity score (Acute Physiology And Chronic Health Evaluation). Co-primary outcome measures were duration of hospital stay and 30-day mortality. Secondary outcomes were stoma formation, stenting completion and complication rates, perioperative morbidity, 6-month survival, 3-year recurrence, resource use, adherence to chemotherapy, and quality of life. Analyses were undertaken by intention to treat. Results Between 23 April 2009 and 22 December 2014, 245 patients from 39 hospitals were randomized. Stenting was attempted in 119 of 123 allocated patients (96.7 per cent), achieving relief of obstruction in 98 of 119 (82.4 per cent). For the 89 per cent treated with curative intent, there were no significant differences in 30-day postoperative mortality (3.6 per cent (4 of 110) versus 5.6 per cent (6 of 107); P = 0.48), or duration of hospital stay (median 19 (i.q.r. 11–34) versus 18 (10–28) days; P = 0.94) between stenting followed by delayed elective surgery and emergency surgery. Among patients undergoing potentially curative treatment, stoma formation occurred less frequently in those allocated to stenting than those allocated to immediate surgery (47 of 99 (47.5 per cent) versus 72 of 106 (67.9 per cent); P = 0.003). There were no significant differences in perioperative morbidity, critical care use, quality of life, 3-year recurrence or mortality between treatment groups. Conclusion Stenting as a bridge to surgery reduces stoma formation without detrimental effects. Registration number: ISRCTN13846816 (http://www.controlled-trials.com)

Critical care usage after major gastrointestinal and liver surgery: a prospective, multicentre observational study

Background Patient selection for critical care admission must balance patient safety with optimal resource allocation. This study aimed to determine the relationship between critical care admission, and postoperative mortality after abdominal surgery. Methods This prespecified secondary analysis of a multicentre, prospective, observational study included consecutive patients enrolled in the DISCOVER study from UK and Republic of Ireland undergoing major gastrointestinal and liver surgery between October and December 2014. The primary outcome was 30-day mortality. Multivariate logistic regression was used to explore associations between critical care admission (planned and unplanned) and mortality, and inter-centre variation in critical care admission after emergency laparotomy. Results Of 4529 patients included, 37.8% (n=1713) underwent planned critical care admissions from theatre. Some 3.1% (n=86/2816) admitted to ward-level care subsequently underwent unplanned critical care admission. Overall 30-day mortality was 2.9% (n=133/4519), and the risk-adjusted association between 30-day mortality and critical care admission was higher in unplanned [odds ratio (OR): 8.65, 95% confidence interval (CI): 3.51–19.97) than planned admissions (OR: 2.32, 95% CI: 1.43–3.85). Some 26.7% of patients (n=1210/4529) underwent emergency laparotomies. After adjustment, 49.3% (95% CI: 46.8–51.9%, P<0.001) were predicted to have planned critical care admissions, with 7% (n=10/145) of centres outside the 95% CI. Conclusions After risk adjustment, no 30-day survival benefit was identified for either planned or unplanned postoperative admissions to critical care within this cohort. This likely represents appropriate admission of the highest-risk patients. Planned admissions in selected, intermediate-risk patients may present a strategy to mitigate the risk of unplanned admission. Substantial inter-centre variation exists in planned critical care admissions after emergency laparotomies

Enhanced performance in fusion plasmas through turbulence suppression by megaelectronvolt ions

© 2022, The Author(s), under exclusive licence to Springer Nature Limited.Alpha particles with energies on the order of megaelectronvolts will be the main source of plasma heating in future magnetic confinement fusion reactors. Instead of heating fuel ions, most of the energy of alpha particles is transferred to electrons in the plasma. Furthermore, alpha particles can also excite Alfvénic instabilities, which were previously considered to be detrimental to the performance of the fusion device. Here we report improved thermal ion confinement in the presence of megaelectronvolts ions and strong fast ion-driven Alfvénic instabilities in recent experiments on the Joint European Torus. Detailed transport analysis of these experiments reveals turbulence suppression through a complex multi-scale mechanism that generates large-scale zonal flows. This holds promise for more economical operation of fusion reactors with dominant alpha particle heating and ultimately cheaper fusion electricity.N

Disruption prediction with artificial intelligence techniques in tokamak plasmas

In nuclear fusion reactors, plasmas are heated to very high temperatures of more than 100 million kelvin and, in so-called tokamaks, they are confined by magnetic fields in the shape of a torus. Light nuclei, such as deuterium and tritium, undergo a fusion reaction that releases energy, making fusion a promising option for a sustainable and clean energy source. Tokamak plasmas, however, are prone to disruptions as a result of a sudden collapse of the system terminating the fusion reactions. As disruptions lead to an abrupt loss of confinement, they can cause irreversible damage to present-day fusion devices and are expected to have a more devastating effect in future devices. Disruptions expected in the next-generation tokamak, ITER, for example, could cause electromagnetic forces larger than the weight of an Airbus A380. Furthermore, the thermal loads in such an event could exceed the melting threshold of the most resistant state-of-the-art materials by more than an order of magnitude. To prevent disruptions or at least mitigate their detrimental effects, empirical models obtained with artificial intelligence methods, of which an overview is given here, are commonly employed to predict their occurrence—and ideally give enough time to introduce counteracting measures