Functional Groups Based on Leaf Physiology: Are they Spatially and Temporally Robust?

The functional grouping hypothesis, which suggests that complexity in ecosystem function can be simplified by grouping species with similar responses, was tested in the Florida scrub habitat. Functional groups were identified based on how species in fire maintained Florida scrub regulate exchange of carbon and water with the atmosphere as indicated by both instantaneous gas exchange measurements and integrated measures of function (%N, delta C-13, delta N-15, C-N ratio). Using cluster analysis, five distinct physiologically-based functional groups were identified in the fire maintained scrub. These functional groups were tested to determine if they were robust spatially, temporally, and with management regime. Analysis of Similarities (ANOSIM), a non-parametric multivariate analysis, indicated that these five physiologically-based groupings were not altered by plot differences (R = -0.115, p = 0.893) or by the three different management regimes; prescribed burn, mechanically treated and burn, and fire-suppressed (R = 0.018, p = 0.349). The physiological groupings also remained robust between the two climatically different years 1999 and 2000 (R = -0.027, p = 0.725). Easy-to-measure morphological characteristics indicating functional groups would be more practical for scaling and modeling ecosystem processes than detailed gas-exchange measurements, therefore we tested a variety of morphological characteristics as functional indicators. A combination of non-parametric multivariate techniques (Hierarchical cluster analysis, non-metric Multi-Dimensional Scaling, and ANOSIM) were used to compare the ability of life form, leaf thickness, and specific leaf area classifications to identify the physiologically-based functional groups. Life form classifications (ANOSIM; R = 0.629, p 0.001) were able to depict the physiological groupings more adequately than either specific leaf area (ANOSIM; R = 0.426, p = 0.001) or leaf thickness (ANOSIM; R 0.344, p 0.001). The ability of life forms to depict the physiological groupings was improved by separating the parasitic Ximenia americana from the shrub category (ANOSIM; R = 0.794, p = 0.001). Therefore, a life form classification including parasites was determined to be a good indicator of the physiological processes of scrub species, and would be a useful method of grouping for scaling physiological processes to the ecosystem level

The Effects of Vegetative Type, Edges, Fire History, Rainfall and Management in Fire-Maintained Ecosystems

The combined effects of repeated fires, climate, and landscape features (e.g., edges) need greater focus in fire ecology studies, which usually emphasize characteristics of the most recent fire and not fire history. Florida scrub-jays are an imperiled, territorial species that prefer medium (1.2-1.7 m) shrub heights. We measured short, medium, and tall habitat quality states annually within 10 ha grid cells that represented potential territories because frequent fires and vegetative recovery cause annual variation in habitat quality. We used multistate models and model selection to test competing hypotheses about how transition probabilities between states varied annually as functions of environmental covariates. Covariates included vegetative type, edges, precipitation, openings (gaps between shrubs), mechanical cutting, and fire characteristics. Fire characteristics not only included an annual presenceabsence of fire covariate, but also fire history covariates: time since the previous fire, the maximum fire-free interval, and the number of repeated fires. Statistical models with support included many covariates for each transition probability, often including fire history, interactions and nonlinear relationships. Tall territories resulted from 28 years of fire suppression and habitat fragmentation that reduced the spread of fires across landscapes. Despite 35 years of habitat restoration and prescribed fires, half the territories remained tall suggesting a regime shift to a less desirable habitat condition. Measuring territory quality states and environmental covariates each year combined with multistate modeling provided a useful empirical approach to quantify the effects of repeated fire in combinations with environmental variables on transition probabilities that drive management strategies and ecosystem change

The Effects of Vegetative Type, Edges, Fire History, Rainfall and Management in Fire-Maintained Habitat

The combined effects of fire history, climate, and landscape features (e.g., edges) on habitat specialists need greater focus in fire ecology studies, which usually only emphasize characteristics of the most recent fire. Florida scrub-jays are an imperiled, territorial species that prefer medium (1.2-1.7 m) shrub heights, which are dynamic because of frequent fires. We measured short, medium, and tall habitat quality states annually within 10 ha grid cells (that represented potential territories) because fires and vegetative recovery cause annual variation in habitat quality. We used multistate models and model selection to test competing hypotheses about how transition probabilities vary between states as functions of environmental covariates. Covariates included vegetative type, edges (e.g., roads, forests), precipitation, openings (gaps between shrubs), mechanical cutting, and fire characteristics. Fire characteristics not only included an annual presence/absence of fire covariate, but also fire history covariates: time since the previous fire, the longest fire-free interval, and the number of repeated fires. Statistical models with support included many covariates for each transition probability, often including fire history, interactions and nonlinear relationships. Tall territories resulted from 28 years of fire suppression and habitat fragmentation that reduced the spread of fires across landscapes. Despite 35 years of habitat restoration and prescribed fires, half the territories remained tall suggesting a regime shift to a less desirable habitat condition. Edges reduced the effectiveness of fires in setting degraded scrub and flatwoods into earlier successional states making mechanical cutting an important tool to compliment frequent prescribed fires

Ecological Impacts of the Space Shuttle Program at John F. Kennedy Space Center, Florida

The Space Shuttle Program was one of NASAs first major undertakings to fall under the environmental impact analysis and documentation requirements of the National Environmental Policy Act of 1969 (NEPA). Space Shuttle Program activities at John F. Kennedy Space Center (KSC) and the associated Merritt Island National Wildlife Refuge (MINWR) contributed directly and indirectly to both negative and positive ecological trends in the region through the long-term, stable expenditure of resources over the 40 year program life cycle. These expenditures provided support to regional growth and development in conjunction with other sources that altered land use patterns, eliminated and modified habitats, and contributed to cultural eutrophication of the Indian River Lagoon. At KSC, most Space Shuttle Program related actions were conducted in previously developed facilities and industrial areas with the exception of the construction of the shuttle landing facility (SLF) and the space station processing facility (SSPF). Launch and operations impacts were minimal as a result of the low annual launch rate. The majority of concerns identified during the NEPA process such as potential weather modification, acid rain off site, and local climate change did not occur. Launch impacts from deposition of HCl and particulates were assimilated as a result of the high buffering capacity of the system and low launch and loading rates. Metals deposition from exhaust deposition did not display acute impacts. Sub-lethal effects are being investigated as part of the Resource Conservation and Recovery Act (RCRA) regulatory process. Major positive Space Shuttle Program effects were derived from the adequate resources available at the Center to implement the numerous environmental laws and regulations designed to enhance the quality of the environment and minimize impacts from human activities. This included reduced discharges of domestic and industrial wastewater, creation of stormwater management systems, remediation of past contamination sites, implementation of hazardous waste management systems, and creation of a culture of sustainability. Working with partners such as the USFWS and the St Johns River Water Management District (SJRWMD), wetlands and scrub restoration and management initiatives were implemented to enhance fish and wildlife populations at the Center. KSC remains the single largest preserve on the east coast of Florida in part due to NASAs commitment to stewardship. Ongoing Ecological Program projects are directed at development of information and knowledge to address future KSC management questions including the transition to a joint government and commercial launch facility, enhanced habitat management requirements for wetlands and scrub, potential impacts of emerging contaminants, and adaptation to climate change including projected sea level rise over the next 50-75 years

Somatic activating mutations in Pik3ca cause sporadic venous malformations in mice and humans.

Venous malformations (VMs) are painful and deforming vascular lesions composed of dilated vascular channels, which are present from birth. Mutations in the TEK gene, encoding the tyrosine kinase receptor TIE2, are found in about half of sporadic (nonfamilial) VMs, and the causes of the remaining cases are unknown. Sclerotherapy, widely accepted as first-line treatment, is not fully efficient, and targeted therapy for this disease remains underexplored. We have generated a mouse model that faithfully mirrors human VM through mosaic expression of Pik3ca(H1047R), a constitutively active mutant of the p110α isoform of phosphatidylinositol 3-kinase (PI3K), in the embryonic mesoderm. Endothelial expression of Pik3ca(H1047R)resulted in endothelial cell (EC) hyperproliferation, reduction in pericyte coverage of blood vessels, and decreased expression of arteriovenous specification markers. PI3K pathway inhibition with rapamycin normalized EC hyperproliferation and pericyte coverage in postnatal retinas and stimulated VM regression in vivo. In line with the mouse data, we also report the presence of activating PIK3CA mutations in human VMs, mutually exclusive with TEK mutations. Our data demonstrate a causal relationship between activating Pik3ca mutations and the genesis of VMs, provide a genetic model that faithfully mirrors the normal etiology and development of this human disease, and establish the basis for the use of PI3K-targeted therapies in VMs.Postdoctoral fellowships were from EMBO (A LTF 165-2013) to S.D.C, EU Marie Curie (MEIF-CT-2005-010264) to E.T. and EU Marie Curie (PIIF-GA-2009-252846) to I.M.B. M.Z.-T. is supported by the EPSRC Early Career Fellowship of T.L.K. (EP/L006472/1). D.J.S. is a BHF Intermediate Basic Science Research Fellow (FS/15/33/31608). A.L.D is supported by the UK NIHR Joint UCL/University College London Hospitals Biomedical Research Centre. V.E.R.P. was supported by the Wellcome Trust (097721/Z/11/Z). R.K.S. is supported by the Wellcome Trust (WT098498), the Medical Research Council (M RC_MC_UU_12012/5). R.G.K. is supported by the NIHR Rare Diseases Translational Research Collaboration. V.W. is supported by the European FPVI Integrated Project ‘Eurostemcell’. M.F.L. and A.B. are supported by the King’s College London and UCL Comprehensive Cancer Imaging Centre CR-UK and EPSRC, in association with the MRC and DoH (England). W.A.P. is supported by funding from the National Health and Medical Research Council (NHMRC) of Australia. Work in the laboratory of M.G. is supported by research grants SAF2013-46542-P and SAF2014-59950-P from MICINN (Spain), 2014-SGR-725 from the Catalan Government, the People Programme (Marie Curie Actions) from the European Union's Seventh Framework Programme FP7/2007-2013/ (REA grant agreement 317250), the Institute of Health Carlos III (ISC III) and the European Regional Development Fund (ERDF) under the integrated Project of Excellence no. PIE13/00022 (ONCOPROFILE). Work in the laboratory of B.V. is supported by Cancer Research UK (C23338/A15965) and the UK NIHR University College London Hospitals Biomedical Research Centre.This is the author accepted manuscript. The final version is available from the American Association for the Advancement of Science via http://dx.doi.org/10.1126/scitranslmed.aad998

A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem

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

Implementation of corticosteroids in treating COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK:prospective observational cohort study

BACKGROUND: Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care. METHODS: We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260. FINDINGS: Between June 17, 2020, and April 14, 2021, 47 795 (75·2%) of 63 525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11 185 [86·6%] of 12 909 vs 36 415 [72·4%] of 50 278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0·79 [95% CI 0·70–0·89], p=0·0001, for 70–79 years; 0·52 [0·46–0·58], p80 years), independent of patient demographics and illness severity. 84 (54·2%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27·5% in the week before June 16, 2020, to 75–80% in January, 2021. INTERPRETATION: Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered. FUNDING: UK National Institute for Health Research and UK Medical Research Council

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

Viral coinfections in hospitalized coronavirus disease 2019 patients recruited to the international severe acute respiratory and emerging infections consortium WHO clinical characterisation protocol UK study

Background We conducted this study to assess the prevalence of viral coinfection in a well characterized cohort of hospitalized coronavirus disease 2019 (COVID-19) patients and to investigate the impact of coinfection on disease severity. Methods Multiplex real-time polymerase chain reaction testing for endemic respiratory viruses was performed on upper respiratory tract samples from 1002 patients with COVID-19, aged <1 year to 102 years old, recruited to the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK study. Comprehensive demographic, clinical, and outcome data were collected prospectively up to 28 days post discharge. Results A coinfecting virus was detected in 20 (2.0%) participants. Multivariable analysis revealed no significant risk factors for coinfection, although this may be due to rarity of coinfection. Likewise, ordinal logistic regression analysis did not demonstrate a significant association between coinfection and increased disease severity. Conclusions Viral coinfection was rare among hospitalized COVID-19 patients in the United Kingdom during the first 18 months of the pandemic. With unbiased prospective sampling, we found no evidence of an association between viral coinfection and disease severity. Public health interventions disrupted normal seasonal transmission of respiratory viruses; relaxation of these measures mean it will be important to monitor the prevalence and impact of respiratory viral coinfections going forward