Cerebral challenge

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Land-use change and propagule pressure promote plant invasions in tropical rainforest remnants

Context: Intact tropical rainforests are considered robust to plant invasions. However, land-use change alters the structure and species composition of native forest, opening up tropical landscapes to invasion. Yet, the relative roles of key drivers on tropical forest invasions remain little investigated. Objectives: We examine factors affecting plant invasion of rainforest remnants in oil-palm dominated landscapes in Sabah, Malaysian Borneo. We hypothesized that invasion is greater in highly fragmented landscapes, and in disturbed forests with lower native plant diversity (cf. old-growth rainforests). Methods: Native and exotic plants were surveyed in 47 plots at 17 forest sites, spanning gradients in landscape-scale fragmentation and local forest disturbance. Using partial least squares path-modelling, we examined correlations between invasion, fragmentation, forest disturbance, propagule pressure, soil characteristics and native plant community. Results: We recorded 6999 individuals from 329 genera in total, including eight exotic species (0–51% of individuals/plot, median = 1.4%) representing shrubs, forbs, graminoids and climbers. The best model (R2 = 0.343) revealed that invasion was correlated with disturbance and propagule pressure (high prevalence of exotic species in plantation matrix), the latter being driven by greater fragmentation of the landscape. Our models revealed a significant negative correlation between invasion and native tree seedlings and sapling community diversity. Conclusions: Increasing landscape fragmentation promotes exotic plant invasion in remnant tropical forests, especially if local disturbance is high. The association between exotic species invasion and young native tree community may have impacts for regeneration given that fragmentation is predicted to increase and so plant invasion may become more prevalent

Genetic origins of honey bees (Apis mellifera) on Kangaroo Island and Norfolk Island (Australia) and the Kingdom of Tonga

International audienceAbstractWe examine the origin of honey bee (Apis mellifera) populations in Kangaroo Island (Australia), Norfolk Island (Australia) and the Kingdom of Tonga using a highly polymorphic mitochondrial DNA region and a panel of 37 single nucleotide polymorphisms that assigns ancestry to three evolutionary lineages: Eastern Europe, Western Europe and Africa. We also examine inbreeding coefficients and genetic variation using microsatellites and mitochondrial sequencing. The honey bees of Kangaroo Island have a high proportion of Eastern European ancestry (90.2%), consistent with claims that they are of the subspecies A. m. ligustica. The honey bees of Norfolk Island also had a majority of ancestry from Eastern Europe (73.1%) with some contribution from Western Europe (21.2%). The honey bees of Tonga are mainly of Western European (70.3%) origin with some Eastern European ancestry (27.4%). Despite the suspected severe bottlenecks experienced by these island population, inbreeding coefficients were low

Trait filtering during exotic plant invasion of tropical rainforest remnants along a disturbance gradient

1. Human‐modified tropical landscapes are often invaded by exotic plant species, but relatively few species are able to colonise remnant areas of rainforest embedded within such landscapes. The functional traits of successful invaders of natural versus anthropogenic habitats are poorly known, especially in tropical regions, and identifying such traits provides insight into the mechanisms that drive invasion. Here, we examine the invasion of tropical rainforest remnants along a disturbance gradient, within a human‐modified agricultural landscape, and determine whether exotic species that invade these forests are selected according to particular traits. 2. We surveyed the occurrence of 18 exotic species along 100‐m transects in four habitats—oil palm road, forest‐oil palm edges and disturbed and intact forest within rainforest remnants—at 21 sites across Sabah, Malaysian Borneo. We collated data on four functional traits relevant to the barriers plants encounter when colonising new environments (e.g. dispersal and persistence) and tested whether trait filtering occurs during invasion of rainforest remnants. 3. Exotic species richness declined significantly from oil palm (mean 9.2 species per transect) to forest edge (7.8 species) to inside rainforest remnants (3.1 species in disturbed forest), and only one species, Clidemia hirta, invaded intact forest. Exotic communities within rainforest remnants had long‐distance (vertebrate) dispersal, were woodier and had taller maximum heights, compared to those found in oil palm. For each trait, the community‐weighted mean for the forest edge community was intermediate between oil palm and disturbed forest, suggesting trait filtering during the invasion of rainforest remnants. 4. Our study provides strong evidence that trait filtering occurs during invasion from human‐modified agricultural habitats into previously disturbed forests via the forest edge. Successful invasion of rainforest remnants requires relatively long‐distance dispersal, in particular by vertebrates, as well as traits that are more similar to those of native forest species (i.e. tall and woody), making these exotic species more able to compete and persist in that environment. Our results show that disturbed tropical rainforests with open canopies are susceptible to invasion and highlight the traits of exotic species which can invade rainforest habitats, and which may pose a threat to regenerating tropical rainforests

Cryptic Eimeria genotypes are common across the southern but not northern hemisphere

The phylum Apicomplexa includes parasites of medical, zoonotic and veterinary significance. Understanding the global distribution and genetic diversity of these protozoa is of fundamental importance for efficient, robust and long-lasting methods of control. Eimeria spp. cause intestinal coccidiosis in all major livestock animals and are the most important parasites of domestic chickens in terms of both economic impact and animal welfare. Despite having significant negative impacts on the efficiency of food production, many fundamental questions relating to the global distribution and genetic variation of Eimeria spp. remain largely unanswered. Here, we provide the broadest map yet of Eimeria occurrence for domestic chickens, confirming that all the known species (Eimeria acervulina, Eimeria brunetti, Eimeria maxima, Eimeria mitis, Eimeria necatrix, Eimeria praecox, Eimeria tenella) are present in all six continents where chickens are found (including 21 countries). Analysis of 248 internal transcribed spacer sequences derived from 17 countries provided evidence of possible allopatric diversity for species such as E. tenella (FST values ⩽0.34) but not E. acervulina and E. mitis, and highlighted a trend towards widespread genetic variance. We found that three genetic variants described previously only in Australia and southern Africa (operational taxonomic units x, y and z) have a wide distribution across the southern, but not the northern hemisphere. While the drivers for such a polarised distribution of these operational taxonomic unit genotypes remains unclear, the occurrence of genetically variant Eimeria may pose a risk to food security and animal welfare in Europe and North America should these parasites spread to the northern hemisphere

Creating a Next Generation Phenotype Library : the health data research UK Phenotype Library

Open Access via the OUP AgreementPeer reviewe

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues

Rescue therapy for vasospasm following aneurysmal subarachnoid hemorrhage:a propensity score-matched analysis with machine learning

OBJECTIVE Rescue therapies have been recommended for patients with angiographic vasospasm (aVSP) and delayed cerebral ischemia (DCI) following subarachnoid hemorrhage (SAH). However, there is little evidence from randomized clinical trials that these therapies are safe and effective. The primary aim of this study was to apply game theory-based methods in explainable machine learning (ML) and propensity score matching to determine if rescue therapy was associated with better 3-month outcomes following post-SAH aVSP and DCI. The authors also sought to use these explainable ML methods to identify patient populations that were more likely to receive rescue therapy and factors associated with better outcomes after rescue therapy. METHODS Data for patients with aVSP or DCI after SAH were obtained from 8 clinical trials and 1 observational study in the Subarachnoid Hemorrhage International Trialists repository. Gradient boosting ML models were constructed for each patient to predict the probability of receiving rescue therapy and the 3-month Glasgow Outcome Scale (GOS) score. Favorable outcome was defined as a 3-month GOS score of 4 or 5. Shapley Additive Explanation (SNAP) values were calculated for each patient-derived model to quantify feature importance and interaction effects. Variables with high S HAP importance in predicting rescue therapy administration were used in a propensity score-matched analysis of rescue therapy and 3-month GOS scores. RESULTS The authors identified 1532 patients with aVSP or DCI. Predictive, explainable ML models revealed that aneurysm characteristics and neurological complications, but not admission neurological scores, carried the highest relative importance rankings in predicting whether rescue therapy was administered. Younger age and absence of cerebral ischemia/ infarction were invariably linked to better rescue outcomes, whereas the other important predictors of outcome varied by rescue type (interventional or noninterventional). In a propensity score-matched analysis guided by SHAP-based variable selection, rescue therapy was associated with higher odds of 3-month GOS scores of 4-5 (OR 1.63, 95% CI 1.22-2.17). CONCLUSIONS Rescue therapy may increase the odds of good outcome in patients with aVSP or DCI after SAH. Given the strong association between cerebral ischemia/infarction and poor outcome, trials focusing on preventative or therapeutic interventions in these patients may be most able to demonstrate improvements in clinical outcomes. Insights developed from these models may be helpful for improving patient selection and trial design

Successful awake proning is associated with improved clinical outcomes in patients with COVID-19: single-centre high-dependency unit experience

The SARS-CoV-2 can lead to severe illness with COVID-19. Outcomes of patients requiring mechanical ventilation are poor. Awake proning in COVID-19 improves oxygenation, but on data clinical outcomes is limited. This single-centre retrospective study aimed to assess whether successful awake proning of patients with COVID-19, requiring respiratory support (continuous positive airways pressure (CPAP) or high-flow nasal oxygen (HFNO)) on a respiratory high-dependency unit (HDU), is associated with improved outcomes. HDU care included awake proning by respiratory physiotherapists. Of 565 patients admitted with COVID-19, 71 (12.6%) were managed on the respiratory HDU, with 48 of these (67.6%) requiring respiratory support. Patients managed with CPAP alone 22/48 (45.8%) were significantly less likely to die than patients who required transfer onto HFNO 26/48 (54.2%): CPAP mortality 36.4%; HFNO mortality 69.2%, (p=0.023); however, multivariate analysis demonstrated that increasing age and the inability to awake prone were the only independent predictors of COVID-19 mortality. The mortality of patients with COVID-19 requiring respiratory support is considerable. Data from our cohort managed on HDU show that CPAP and awake proning are possible in a selected population of COVID-19, and may be useful. Further prospective studies are required