Patterns and Drivers of Recent Peatland Carbon Accumulation in Northeastern Canada

Northern peatlands are an important component of the global carbon (C) cycle and have been a net sink of atmospheric C during the Holocene. Under current climate warming conditions, the future sink-source balance of these peatlands is uncertain. In particular, peatlands near the southern limit of permafrost are likely to be sensitive to changes in topography as well as climate. In order to predict how the sink-source balance may change, this thesis focuses on determining the generality of observed patterns of C accumulation in Northeastern Canada. The methodological approach in this thesis is unique. A total of 30 cores were taken from 9 peatlands located in 3 ecoclimatic regions along the North Shore of the Gulf of St Lawrence. This replication of records allows for climate-scale (allogenic) signals to be separated from the internal or local factors (autogenic), and for statistical testing of differences between regions and within sites over time. Trends in carbon accumulation rates (CAR) were analysed on three levels: (1) within individual sites along a hydrological or microtopography gradient, (2) between overall regions located along a climatic or permafrost gradient, and (3) over time on a multi-centennial scale. Lead-210 (210Pb) dating was used throughout the analysis to increase temporal resolution for the last 150-200 years of C accumulation. The method was thoroughly tested from preparation to analysis and found to produce reliable results, comparable with other dating methods. These dates were then used to develop combined age-depth models for longer-term context. Replicated records of 210Pb inventories and fallout rates were also used to address questions of deposition patterns and post-depositional mobility in peat profiles. Total inventories decreased with water table depth, with lichen hummocks having significantly higher inventories. One site also received significantly higher 210Pb deposition than the other two, as it is more sheltered from the Gulf influence. Recent carbon accumulation rates for the 150-year period for all microforms across all regions was 62.1 ± 4.4 g C m-2 a-1, and were highest for Sphagnum hummocks (79.9 ± 8.9 g C m-2 a-1) and lowest for dry lichen hummocks (42.7 ± 6.2 g C m-2 a-1). Patterns and trends at this scale were mainly driven by autogenic processes, including incomplete decomposition in the acrotelm peat. Models of peat accumulation related to acrotelm thickness were found to be overly simplistic, as carbon accumulation for intermediate microforms showed large natural variability driven by changing ecohydrological feedbacks, in part due to permafrost degradation at one of the sites. Over a multi-centennial scale, carbon accumulation rates were driven by a combination of climatic changes and ecohydrological feedbacks due to shifts in the microform configuration in response to permafrost degradation. Changes in carbon accumulation rates were detected and coincided with Little Ice Age temperature/solar minima (including the Spörer, Maunder and Dalton Minima), permafrost degradation since the 1950s, and recent climatic changes in the mid-1990s. Snow cover and exposure of sites and microforms were found to play an important role, rather than solely climatic variables. Rapid Sphagnum re-establishment in post-permafrost degraded features and increasing temperatures meant that carbon accumulation was highest for the northernmost site in the transect. Age-depth models using a combination of lead-210 and radiocarbon dates allowed for the calculation of carbon accumulation rates at a decadal resolution. While peat carbon sequestration is projected to increase in northern regions, the fate of peatland C near the southern limit of permafrost is complex. Future studies seeking to interpret recent changes should include multiple cores and consider both regional climatic and local ecohydrological drivers.College of Life and Environmental Sciences, University of ExeterUniversité du Québec à Montreal (UQAM

Panton-Valentine leucocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial GWAS

Pyomyositis is a severe bacterial infection of skeletal muscle, commonly affecting children in tropical regions, predominantly caused by . To understand the contribution of bacterial genomic factors to pyomyositis, we conducted a genome-wide association study of cultured from 101 children with pyomyositis and 417 children with asymptomatic nasal carriage attending the Angkor Hospital for Children, Cambodia. We found a strong relationship between bacterial genetic variation and pyomyositis, with estimated heritability 63.8% (95% CI 49.2-78.4%). The presence of the Panton-Valentine leucocidin (PVL) locus increased the odds of pyomyositis 130-fold (=10). The signal of association mapped both to the PVL-coding sequence and the sequence immediately upstream. Together these regions explained over 99.9% of heritability (95% CI 93.5-100%). Our results establish staphylococcal pyomyositis, like tetanus and diphtheria, as critically dependent on a single toxin and demonstrate the potential for association studies to identify specific bacterial genes promoting severe human disease

Quality of care assessment in geriatric evaluation and management units: construction of a chart review tool for a tracer condition

<p>Abstract</p> <p>Background</p> <p>The number of elderly people requiring hospital care is growing, so, quality and assessment of care for elders are emerging and complex areas of research. Very few validated and reliable instruments exist for the assessment of quality of acute care in this field. This study's objective was to create such a tool for Geriatric Evaluation and Management Units (GEMUs).</p> <p>Methods</p> <p>The methodology involved a reliability and feasibility study of a retrospective chart review on 934 older inpatients admitted in 49 GEMUs during the year 2002–2003 for fall-related trauma as a tracer condition. Pertinent indicators for a chart abstraction tool, the Geriatric Care Tool (GCT), were developed and validated according to five dimensions: access to care, comprehensiveness, continuity of care, patient-centred care and appropriateness. Consensus methods were used to develop the content. Participants were experts representing eight main health care professions involved in GEMUs from 19 different sites. Items associated with high quality of care at each step of the multidisciplinary management of patients admitted due to falls were identified. The GCT was tested for intra- and inter-rater reliability using 30 medical charts reviewed by each of three independent and blinded trained nurses. Kappa and agreement measures between pairs of chart reviewers were computed on an item-by-item basis.</p> <p>Results</p> <p>Three quarters of 169 items identifying the process of care, from the case history to discharge planning, demonstrated good agreement (kappa greater than 0.40 and agreement over 70%). Indicators for the appropriateness of care showed less reliability.</p> <p>Conclusion</p> <p>Content validity and reliability results, as well as the feasibility of the process, suggest that the chart abstraction tool can gather standardized and pertinent clinical information for further evaluating quality of care in GEMU using admission due to falls as a tracer condition. However, the GCT should be evaluated in other models of acute geriatric units and new strategies should be developed to improve reliability of peer assessments in characterizing the quality of care for elderly patients with complex conditions.</p

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys

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