A short guide to using British and Irish plant occurrence data for research

A check list of things to ask when using British and Irish plant occurrence data for analyses. Note that many of the issues discussed here may also apply to datasets of animal occurrence data, and to data from other territories

Simple methods for improving the communication of uncertainty in species’ temporal trends

Temporal trends in species occupancy or abundance are a fundamental source of information for ecology and conservation. Model-based uncertainty in these trends is often communicated as frequentist confidence or Bayesian credible intervals, however, these are often misinterpreted in various ways, even by scientists. Research from the science of information visualisation indicates that line ensemble approaches that depict multiple outcomes compatible with a fitted model or data may be superior for the clear communication of model-based uncertainty. The discretisation of continuous probability information into frequency bins has also been shown to be useful for communicating with non-specialists. We present a simple and widely applicable approach that combines these two ideas, and which can be used to clearly communicate model-based uncertainty in species trends (or composite indicators) to stakeholders. We also show how broader ontological uncertainty can be communicated via trend plots using risk-of-bias visualisation approaches developed in other disciplines. The techniques are demonstrated using the example of long-term plant distributional change in Britain, but are applicable to any temporal data consisting of averages and associated uncertainty measures. Our approach supports calls for full transparency in the scientific process by clearly displaying the multiple sources of uncertainty that can be estimated by researchers

With a Little Help from My Friends: Profiles of Perceived Social Support and Their Associations with Adolescent Mental Health

This study investigated profiles of perceived social support and their associations with mental health indicators for male and female adolescents. The sample was a nationally representative group of Danish adolescents age 13–16 years (Male N = 1114; Female N = 1065). Latent profile analysis was used to identify profiles of perceived social support from different sources (classmate, teacher, family, friend). Three distinct profiles of perceived social support were identified for both genders: ‘High’ support from all sources (54.4% of males; 55.5% of females), ‘Moderate’ support from all sources (31.6% of males; 28.8% of females) and ‘Low friend’ support with moderate support from other sources (13.9% of males; 15.7% of females). The ‘high’ perceived support profile was associated with optimal mental health; the ‘moderate’ perceived support profile was associated with lower wellbeing and more frequent emotional symptoms; and the ‘low friend’ perceived support profile was associated with the lowest levels of wellbeing and, specifically for females, higher frequency of emotional symptoms. Results highlight typical profiles of perceived social support among adolescents, and demonstrate nuanced associations between perceived social support and mental health indicators, with notable gender differences

New insights into the genetic etiology of Alzheimer's disease and related dementias.

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

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

Plant atlas 2020: mapping changes in the distribution of the British and Irish flora

Plant Atlas 2020 presents the results of field surveys by the Botanical Society of Britain and Ireland, building on past atlas surveys undertaken by the Botanical Society in the early and late twentieth century. Drawing on the work of thousands of botanists who covered the entirety of Britain and Ireland between 2000 and 2019, this two-volume book features introductory chapters that provide a detailed assessment of the changes to the region’s flora over the past hundred years. Distribution maps and accompanying text and graphics display the phenology, altitudinal range, and time-series trends for 2,616 native and alien species and 247 hybrids. With more than 30 million records gathered during the project, Plant Atlas 2020 will serve as an essential resource for the study and conservation of these wild plants and their vitally important habitats for decades to come. Jointly published with Princeton University Press

Plant Atlas 2020 — British and Irish phenological data (flowering and leafing ranges)

Plant Atlas 2020 is the most comprehensive survey of plants (flowering plants, ferns and charophytes) ever undertaken in Britain and Ireland. It is based on over 30 million records, collected mainly by volunteer recorders of the Botanical Society of Britain and Ireland (BSBI) between 2000 and 2019, as well as previous nationwide surveys undertaken in the 1950s and 1990s. This resource provides the data behind the phenological diagrams (flowering and leafing) presented on the Plant Atlas 2020 website (www.plantatlas2020.org) and in the Plant Atlas 2020 book. Note that for non-flowering plants included in the atlas (e.g. ferns, horsetails etc.), the “flowering” fields in the phenology file included here are equivalent to the months when spore-bearing structures are visible