Estimation and validation of InSAR-derived surface displacements at temperate raised peatlands

Peatland surface motion derived from satellite-based Interferometry of Synthetic Aperture Radar (InSAR) is potentially a proxy for groundwater level variations and greenhouse gas emissions from peat soils. Ground validation of these motions at equivalent temporal resolution has proven problematic, either because of limitations of traditional surveying methods or because of limitations with past InSAR time-series approaches. Novel camera-based instrumentation has enabled in-situ measurement of peat surface from mid-2019 to mid-2022 at two large temperate raised bogs undergoing restoration – Cors Fochno and Cors Caron, in mid-Wales, United Kingdom. The cameras provided continuous measurements at sub-millimetre precision and sub-daily temporal resolution. From these data and Sentinel-1 acquisitions spanning mid-2015 to early-2023, we demonstrate that accurate peat surface motion can be derived by InSAR when a combination of interferometric networks with long and short temporal baselines is used. The InSAR time series data closely match the in-situ data at both bogs, and in particular recover well the annual peat surface oscillations of 10-40 mm. Pearson's values for the point-wise correlation of in-situ and InSAR displacements are 0.8–0.9, while 76% of differences are < ±5 mm and 93% are < ±10 mm. RMSE values between multi-annual in-situ and InSAR peat surface displacement rates are ~7 mm·yr−1 and decrease to ∼3.5 mm for individual peat surface motion measurements. Larger differences mainly occur during drought periods. Multi-annual displacement velocities rates based on InSAR indicate long-term subsidence at Cors Caron (maximum −7 mm·yr−1), while Cors Fochno exhibits subsidence at the centre and uplift at the margins (−9 mm·yr−1 to +5 mm·yr−1). Because of the annual peat surface oscillations, however, more robust ground validation of the long-term peat surface motion rates derived from InSAR requires longer time-series of in-situ measurements than are presently available. Nonetheless, the InSAR-derived surface motion rates correlate well spatially with both peat dome elevation and peat thickness. In addition, the annual oscillations in surface motion are synchronous with or lag slightly behind groundwater level changes. A coarse ratio of 10:1 is observed between annual changes in groundwater level and peat surface displacement. Satellite-based InSAR derived from a fusion of short- and long-term temporal baseline networks can thus enable accurate monitoring of hydrologically driven surface motions of moderately degraded to intact temperate raised peatlands

A rise in the frequency of lasR mutant Pseudomonas aeruginosa among keratitis isolates between 1993 and 2021

IntroductionPseudomonas aeruginosa causes vision threatening keratitis. The LasR transcription factor regulates virulence factors in response to the quorum sensing molecule N-3-oxo-dodecanoyl-L-homoserine lactone. P. aeruginosa isolates with lasR mutations are characterized by an iridescent high sheen phenotype caused by a build-up of 2-heptyl-4-quinolone. A previous study demonstrated 22% (n=101) of P. aeruginosa keratitis isolates from India between 2010 and 2016 were sheen positive lasR mutants, and the sheen phenotype correlated with worse clinical outcomes for patients. In this study, a longitudinal collection of P. aeruginosa keratitis isolates from Eastern North America were screened for lasR mutations by the sheen phenotype and sequencing of the lasR gene.MethodsKeratitis isolates (n=399) were classified by sheen phenotype. The lasR gene was cloned from a subset of isolates, sequenced, and tested for loss of function or dominant-negative status based on an azocasein protease assay. A retrospective chart review compared outcomes of keratitis patients infected by sheen positive and negative isolates.ResultsA significant increase in sheen positive isolates was observed between 1993 and 2021. Extracellular protease activity was reduced among the sheen positive isolates and a defined lasR mutant. Cloned lasR alleles from the sheen positive isolates were loss of function or dominant negative and differed in sequence from previously reported ocular lasR mutant alleles. Retrospective analysis of patient information suggested significantly better visual outcomes for patients infected by sheen positive isolates.DiscussionThese results indicate an increase in lasR mutations among keratitis isolates in the United States and suggest that endemic lasR mutants can cause keratitis

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

State of the climate in 2010

Several large-scale climate patterns influenced climate conditions and weather patterns across the globe during 2010. The transition from a warm El Nino phase at the beginning of the year to a cool La Nina phase by July contributed to many notable events, ranging from record wetness across much of Australia to historically low Eastern Pacific basin and near-record high North Atlantic basin hurricane activity. The remaining five main hurricane basins experienced below-to well-below-normal tropical cyclone activity. The negative phase of the Arctic Oscillation was a major driver of Northern Hemisphere temperature patterns during 2009/10 winter and again in late 2010. It contributed to record snowfall and unusually low temperatures over much of northern Eurasia and parts of the United States, while bringing above-normal temperatures to the high northern latitudes. The February Arctic Oscillation Index value was the most negative since records began in 1950. The 2010 average global land and ocean surface temperature was among the two warmest years on record. The Arctic continued to warm at about twice the rate of lower latitudes. The eastern and tropical Pacific Ocean cooled about 1 C from 2009 to 2010, reflecting the transition from the 2009/10 El Nino to the 2010/11 La Nina. Ocean heat fluxes contributed to warm sea surface temperature anomalies in the North Atlantic and the tropical Indian and western Pacific Oceans. Global integrals of upper ocean heat content for the past several years have reached values consistently higher than for all prior times in the record, demonstrating the dominant role of the ocean in the Earth's energy budget. Deep and abyssal waters of Antarctic origin have also trended warmer on average since the early 1990s. Lower tropospheric temperatures typically lag ENSO surface fluctuations by two to four months, thus the 2010 temperature was dominated by the warm phase El Nino conditions that occurred during the latter half of 2009 and early 2010 and was second warmest on record. The stratosphere continued to be anomalously cool. Annual global precipitation over land areas was about five percent above normal. Precipitation over the ocean was drier than normal after a wet year in 2009. Overall, saltier (higher evaporation) regions of the ocean surface continue to be anomalously salty, and fresher (higher precipitation) regions continue to be anomalously fresh. This salinity pattern, which has held since at least 2004, suggests an increase in the hydrological cycle. Sea ice conditions in the Arctic were significantly different than those in the Antarctic during the year. The annual minimum ice extent in the Arctic reached in September was the third lowest on record since 1979. In the Antarctic, zonally averaged sea ice extent reached an all-time record maximum from mid-June through late August and again from mid-November through early December. Corresponding record positive Southern Hemisphere Annular Mode Indices influenced the Antarctic sea ice extents. Greenland glaciers lost more mass than any other year in the decade-long record. The Greenland Ice Sheet lost a record amount of mass, as the melt rate was the highest since at least 1958, and the area and duration of the melting was greater than any year since at least 1978. High summer air temperatures and a longer melt season also caused a continued increase in the rate of ice mass loss from small glaciers and ice caps in the Canadian Arctic. Coastal sites in Alaska show continuous permafrost warming and sites in Alaska, Canada, and Russia indicate more significant warming in relatively cold permafrost than in warm permafrost in the same geographical area. With regional differences, permafrost temperatures are now up to 2 C warmer than they were 20 to 30 years ago. Preliminary data indicate there is a high probability that 2010 will be the 20th consecutive year that alpine glaciers have lost mass. Atmospheric greenhouse gas concentrations continued to rise and ozone depleting substances continued to decrease. Carbon dioxide increased by 2.60 ppm in 2010, a rate above both the 2009 and the 1980-2010 average rates. The global ocean carbon dioxide uptake for the 2009 transition period from La Nina to El Nino conditions, the most recent period for which analyzed data are available, is estimated to be similar to the long-term average. The 2010 Antarctic ozone hole was among the lowest 20% compared with other years since 1990, a result of warmer-than-average temperatures in the Antarctic stratosphere during austral winter between mid-July and early September

Characteristics and outcomes of COVID-19 patients admitted to hospital with and without respiratory symptoms

Background: COVID-19 is primarily known as a respiratory illness; however, many patients present to hospital without respiratory symptoms. The association between non-respiratory presentations of COVID-19 and outcomes remains unclear. We investigated risk factors and clinical outcomes in patients with no respiratory symptoms (NRS) and respiratory symptoms (RS) at hospital admission. Methods: This study describes clinical features, physiological parameters, and outcomes of hospitalised COVID-19 patients, stratified by the presence or absence of respiratory symptoms at hospital admission. RS patients had one or more of: cough, shortness of breath, sore throat, runny nose or wheezing; while NRS patients did not. Results: Of 178,640 patients in the study, 86.4&nbsp;% presented with RS, while 13.6&nbsp;% had NRS. NRS patients were older (median age: NRS: 74 vs RS: 65) and less likely to be admitted to the ICU (NRS: 36.7&nbsp;% vs RS: 37.5&nbsp;%). NRS patients had a higher crude in-hospital case-fatality ratio (NRS 41.1&nbsp;% vs. RS 32.0&nbsp;%), but a lower risk of death after adjusting for confounders (HR 0.88 [0.83-0.93]). Conclusion: Approximately one in seven COVID-19 patients presented at hospital admission without respiratory symptoms. These patients were older, had lower ICU admission rates, and had a lower risk of in-hospital mortality after adjusting for confounders

Respiratory support in patients with severe COVID-19 in the International Severe Acute Respiratory and Emerging Infection (ISARIC) COVID-19 study: a prospective, multinational, observational study

Background: Up to 30% of hospitalised patients with COVID-19 require advanced respiratory support, including high-flow nasal cannulas (HFNC), non-invasive mechanical ventilation (NIV), or invasive mechanical ventilation (IMV). We aimed to describe the clinical characteristics, outcomes and risk factors for failing non-invasive respiratory support in patients treated with severe COVID-19 during the first two years of the pandemic in high-income countries (HICs) and low middle-income countries (LMICs). Methods: This is a multinational, multicentre, prospective cohort study embedded in the ISARIC-WHO COVID-19 Clinical Characterisation Protocol. Patients with laboratory-confirmed SARS-CoV-2 infection who required hospital admission were recruited prospectively. Patients treated with HFNC, NIV, or IMV within the first 24 h of hospital admission were included in this study. Descriptive statistics, random forest, and logistic regression analyses were used to describe clinical characteristics and compare clinical outcomes among patients treated with the different types of advanced respiratory support. Results: A total of 66,565 patients were included in this study. Overall, 82.6% of patients were treated in HIC, and 40.6% were admitted to the hospital during the first pandemic wave. During the first 24 h after hospital admission, patients in HICs were more frequently treated with HFNC (48.0%), followed by NIV (38.6%) and IMV (13.4%). In contrast, patients admitted in lower- and middle-income countries (LMICs) were less frequently treated with HFNC (16.1%) and the majority received IMV (59.1%). The failure rate of non-invasive respiratory support (i.e. HFNC or NIV) was 15.5%, of which 71.2% were from HIC and 28.8% from LMIC. The variables most strongly associated with non-invasive ventilation failure, defined as progression to IMV, were high leukocyte counts at hospital admission (OR [95%CI]; 5.86 [4.83-7.10]), treatment in an LMIC (OR [95%CI]; 2.04 [1.97-2.11]), and tachypnoea at hospital admission (OR [95%CI]; 1.16 [1.14-1.18]). Patients who failed HFNC/NIV had a higher 28-day fatality ratio (OR [95%CI]; 1.27 [1.25-1.30]). Conclusions: In the present international cohort, the most frequently used advanced respiratory support was the HFNC. However, IMV was used more often in LMIC. Higher leucocyte count, tachypnoea, and treatment in LMIC were risk factors for HFNC/NIV failure. HFNC/NIV failure was related to worse clinical outcomes, such as 28-day mortality. Trial registration This is a prospective observational study; therefore, no health care interventions were applied to participants, and trial registration is not applicable

ISARIC-COVID-19 dataset: A Prospective, Standardized, Global Dataset of Patients Hospitalized with COVID-19

The International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) COVID-19 dataset is one of the largest international databases of prospectively collected clinical data on people hospitalized with COVID-19. This dataset was compiled during the COVID-19 pandemic by a network of hospitals that collect data using the ISARIC-World Health Organization Clinical Characterization Protocol and data tools. The database includes data from more than 705,000 patients, collected in more than 60 countries and 1,500 centres worldwide. Patient data are available from acute hospital admissions with COVID-19 and outpatient follow-ups. The data include signs and symptoms, pre-existing comorbidities, vital signs, chronic and acute treatments, complications, dates of hospitalization and discharge, mortality, viral strains, vaccination status, and other data. Here, we present the dataset characteristics, explain its architecture and how to gain access, and provide tools to facilitate its use

Respiratory support in patients with severe COVID-19 in the International Severe Acute Respiratory and Emerging Infection (ISARIC) COVID-19 study: a prospective, multinational, observational study

Background: Up to 30% of hospitalised patients with COVID-19 require advanced respiratory support, including high-flow nasal cannulas (HFNC), non-invasive mechanical ventilation (NIV), or invasive mechanical ventilation (IMV). We aimed to describe the clinical characteristics, outcomes and risk factors for failing non-invasive respiratory support in patients treated with severe COVID-19 during the first two years of the pandemic in high-income countries (HICs) and low middle-income countries (LMICs). Methods: This is a multinational, multicentre, prospective cohort study embedded in the ISARIC-WHO COVID-19 Clinical Characterisation Protocol. Patients with laboratory-confirmed SARS-CoV-2 infection who required hospital admission were recruited prospectively. Patients treated with HFNC, NIV, or IMV within the first 24 h of hospital admission were included in this study. Descriptive statistics, random forest, and logistic regression analyses were used to describe clinical characteristics and compare clinical outcomes among patients treated with the different types of advanced respiratory support. Results: A total of 66,565 patients were included in this study. Overall, 82.6% of patients were treated in HIC, and 40.6% were admitted to the hospital during the first pandemic wave. During the first 24 h after hospital admission, patients in HICs were more frequently treated with HFNC (48.0%), followed by NIV (38.6%) and IMV (13.4%). In contrast, patients admitted in lower- and middle-income countries (LMICs) were less frequently treated with HFNC (16.1%) and the majority received IMV (59.1%). The failure rate of non-invasive respiratory support (i.e. HFNC or NIV) was 15.5%, of which 71.2% were from HIC and 28.8% from LMIC. The variables most strongly associated with non-invasive ventilation failure, defined as progression to IMV, were high leukocyte counts at hospital admission (OR [95%CI]; 5.86 [4.83–7.10]), treatment in an LMIC (OR [95%CI]; 2.04 [1.97–2.11]), and tachypnoea at hospital admission (OR [95%CI]; 1.16 [1.14–1.18]). Patients who failed HFNC/NIV had a higher 28-day fatality ratio (OR [95%CI]; 1.27 [1.25–1.30]). Conclusions: In the present international cohort, the most frequently used advanced respiratory support was the HFNC. However, IMV was used more often in LMIC. Higher leucocyte count, tachypnoea, and treatment in LMIC were risk factors for HFNC/NIV failure. HFNC/NIV failure was related to worse clinical outcomes, such as 28-day mortality. Trial registration This is a prospective observational study; therefore, no health care interventions were applied to participants, and trial registration is not applicable