Earth Science Education #7. GeoTrails: Accessible Online Tools for Outreach and Education

As geoscientists, we must prioritize improving our ability to communicate science to the public. Effective geoscience communication enables communities to understand how geological processes have shaped our planet and make informed decisions about Earth’s future. However, geoscience research outputs have traditionally been published in peer-reviewed journals and presented at academic conferences. Consequently, essential information about local geology is rarely available in accessible, open access, and engaging formats. Here, we propose virtual field trips, or ‘GeoTrails’, as a possible solution to address the disconnect between geoscience research and public knowledge by improving our communication to the public. This initiative is largely driven by undergraduate students, who identify points of geological interest along selected hiking trails, write concise descriptions derived from scientific sources (e.g. longer peer-reviewed articles and government reports), and collect field data (e.g. 3-D LiDAR models, drone photography) to illustrate the characteristics of these geological features. The goal of the project is to communicate the importance of local geology on our environment and to raise awareness of how changing climates could affect us in the future; this information can empower communities to make better, more informed planning decisions. The creation of GeoTrails along the Niagara Escarpment offers a promising strategy to highlight the role of geoscientists and to engage the public in our ongoing research that aims to showcase Canada’s geoheritage.En tant que géoscientifiques, nous devons donner la priorité à l’amélioration de notre capacité à communiquer la science au public. Une communication efficace des géosciences permet aux communautés de comprendre comment les processus géologiques ont façonné notre planète et de prendre des décisions éclairées sur l’avenir de la Terre. Cependant, les résultats de la recherche en géosciences ont traditionnellement été publiés dans des revues à comité de lecture et présentés lors de conférences académiques. Par conséquent, les informations essentielles sur la géologie locale sont rarement disponibles sous des formats accessibles, en libre accès et attrayants. Dans cette optique, nous proposons des excursions virtuelles, ou « GeoTrails », comme solution possible pour combler le fossé entre la recherche en géosciences et la connaissance du public en améliorant notre communication avec celui-ci. Cette initiative est en grande partie menée par des étudiants de premier cycle, qui identifient des points d’intérêt géologiques le long de sentiers de randonnée sélectionnés, rédigent des descriptions concises basées sur des sources scientifiques (par exemple, des articles à comité de lecture plus longs et des rapports gouvernementaux) et collectent des données sur le terrain (par exemple, des modèles LiDAR 3-D, des photographies par drone) pour illustrer les caractéristiques de ces caractéristiques géologiques. L'objectif du projet est de communiquer l'importance de la géologie locale sur notre environnement et de sensibiliser aux façons dont les changements climatiques pourraient nous affecter à l'avenir; cette information peut permettre aux communautés de prendre des décisions de planification meilleures et plus éclairées. La création de GeoTrails le long de l'escarpement du Niagara offre une stratégie prometteuse pour mettre en valeur le rôle des géoscientifiques et pour engager le public dans notre recherche en cours qui vise à présenter le patrimoine géologique du Canada

New multicellular marine macroalgae from the early Tonian of northwestern Canada

Molecular phylogenetic data suggest that photosynthetic eukaryotes first evolved in freshwater environments in the early Proterozoic and diversified into marine environments by the Tonian Period, but early algal evolution is poorly reflected in the fossil record. Here, we report newly discovered, millimeter- to centimeter-scale macrofossils from outershelf marine facies of the ca. 950–900 Ma (Re-Os minimum age constraint = 898 ± 68 Ma) Dolores Creek Formation in the Wernecke Mountains, northwestern Canada. These fossils, variably preserved by iron oxides and clay minerals, represent two size classes. The larger forms feature unbranching thalli with uniform cells, differentiated cell walls, longitudinal striations, and probable holdfasts, whereas the smaller specimens display branching but no other diagnostic features. While the smaller population remains unresolved phylogenetically and may represent cyanobacteria, we interpret the larger fossils as multicellular eukaryotic macroalgae with a plausible green algal affinity based on their large size and presence of rib-like wall ornamentation. Considered as such, the latter are among the few green algae and some of the largest macroscopic eukaryotes yet recognized in the early Neoproterozoic. Together with other Tonian fossils, the Dolores Creek fossils indicate that eukaryotic algae, including green algae, colonized marine environments by the early Neoproterozoic Era

Search for Diffuse Neutral Hydrogen and HI Clouds in the NGC 2403 Group

We have observed the NGC 2403 group of galaxies using the Robert C. Byrd Green Bank Telescope (GBT) in a search for faint, extended neutral hydrogen clouds similar to the clouds found around the M81/M82 group, which is located approximately 250 kpc from the NGC 2403 group along the same filament of galaxies. For an HI cloud with a size < 10 kpc within 50 kpc of a group galaxy, our 7-sigma mass detection limit is 2.2 x 10^6 M_sun for a cloud with a linewidth of 20 km/s, over the velocity range from -890 to 1750 km/s. At this sensitivity level we detect 3 new HI clouds in the direction of the group, as well as the known galaxies. The mean velocity of the new clouds differs from that of the group galaxies by more than 250 km/s, but are in the range of Milky Way High Velocity Clouds (HVCs) in that direction. It is most likely that the clouds are part of the Milky Way HVC population. If HI clouds exist in the NGC 2403 group, their masses are less than 2.2 x 10^6 M_sun. We also compared our results to structures that are expected based on recent cosmological models, and found none of the predicted clouds. If NGC 2403 is surrounded by a population of dark matter halos similar to those proposed for the Milky Way in recent models, our observations imply that their HI content is less than 1% of their total mass.Comment: Accepted by A

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

Determining crystal structures through crowdsourcing and coursework

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

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COMSOL Multiphysics computational fluid dynamics simulation file