The epidemiological impact of the NHS COVID-19 app.

The COVID-19 pandemic has seen the emergence of digital contact tracing to help to prevent the spread of the disease. A mobile phone app records proximity events between app users, and when a user tests positive for COVID-19, their recent contacts can be notified instantly. Theoretical evidence has supported this new public health intervention1-6, but its epidemiological impact has remained uncertain7. Here we investigate the impact of the National Health Service (NHS) COVID-19 app for England and Wales, from its launch on 24 September 2020 to the end of December 2020. It was used regularly by approximately 16.5 million users (28% of the total population), and sent approximately 1.7 million exposure notifications: 4.2 per index case consenting to contact tracing. We estimated that the fraction of individuals notified by the app who subsequently showed symptoms and tested positive (the secondary attack rate (SAR)) was 6%, similar to the SAR for manually traced close contacts. We estimated the number of cases averted by the app using two complementary approaches: modelling based on the notifications and SAR gave an estimate of 284,000 (central 95% range of sensitivity analyses 108,000-450,000), and statistical comparison of matched neighbouring local authorities gave an estimate of 594,000 (95% confidence interval 317,000-914,000). Approximately one case was averted for each case consenting to notification of their contacts. We estimated that for every percentage point increase in app uptake, the number of cases could be reduced by 0.8% (using modelling) or 2.3% (using statistical analysis). These findings support the continued development and deployment of such apps in populations that are awaiting full protection from vaccines.

Differentiation between descending thoracic aortic diseases using machine learning and plasma proteomic signatures.

BACKGROUND: Descending thoracic aortic aneurysms and dissections can go undetected until severe and catastrophic, and few clinical indices exist to screen for aneurysms or predict risk of dissection. METHODS: This study generated a plasma proteomic dataset from 75 patients with descending type B dissection (Type B) and 62 patients with descending thoracic aortic aneurysm (DTAA). Standard statistical approaches were compared to supervised machine learning (ML) algorithms to distinguish Type B from DTAA cases. Quantitatively similar proteins were clustered based on linkage distance from hierarchical clustering and ML models were trained with uncorrelated protein lists across various linkage distances with hyperparameter optimization using fivefold cross validation. Permutation importance (PI) was used for ranking the most important predictor proteins of ML classification between disease states and the proteins among the top 10 PI protein groups were submitted for pathway analysis. RESULTS: Of the 1,549 peptides and 198 proteins used in this study, no peptides and only one protein, hemopexin (HPX), were significantly different at an adjusted p < 0.01 between Type B and DTAA cases. The highest performing model on the training set (Support Vector Classifier) and its corresponding linkage distance (0.5) were used for evaluation of the test set, yielding a precision-recall area under the curve of 0.7 to classify between Type B from DTAA cases. The five proteins with the highest PI scores were immunoglobulin heavy variable 6-1 (IGHV6-1), lecithin-cholesterol acyltransferase (LCAT), coagulation factor 12 (F12), HPX, and immunoglobulin heavy variable 4-4 (IGHV4-4). All proteins from the top 10 most important groups generated the following significantly enriched pathways in the plasma of Type B versus DTAA patients: complement activation, humoral immune response, and blood coagulation. CONCLUSIONS: We conclude that ML may be useful in differentiating the plasma proteome of highly similar disease states that would otherwise not be distinguishable using statistics, and, in such cases, ML may enable prioritizing important proteins for model prediction.

High-Field Asymmetric Waveform Ion Mobility Spectrometry: Practical Alternative for Cardiac Proteome Sample Processing.

Heart tissue sample preparation for mass spectrometry (MS) analysis that includes prefractionation reduces the cellular protein dynamic range and increases the relative abundance of nonsarcomeric proteins. We previously described "IN-Sequence" (IN-Seq) where heart tissue lysate is sequentially partitioned into three subcellular fractions to increase the proteome coverage more than a single direct tissue analysis by mass spectrometry. Here, we report an adaptation of the high-field asymmetric ion mobility spectrometry (FAIMS) coupled to mass spectrometry, and the establishment of a simple one step sample preparation coupled with gas-phase fractionation. The FAIMS approach substantially reduces manual sample handling, significantly shortens the MS instrument processing time, and produces unique protein identification and quantification approximating the commonly used IN-Seq method in less time.

Phylogenetic risk assessment is robust for forecasting the impact of European insects on North American conifers.

Some introduced species cause severe damage, although the majority have little impact. Robust predictions of which species are most likely to cause substantial impacts could focus efforts to mitigate those impacts or prevent certain invasions entirely. Introduced herbivorous insects can reduce crop yield, fundamentally alter natural and managed forest ecosystems, and are unique among invasive species in that they require certain host plants to succeed. Recent studies have demonstrated that understanding the evolutionary history of introduced herbivores and their host plants can provide robust predictions of impact. Specifically, divergence times between hosts in the native and introduced ranges of a nonnative insect can be used to predict the potential impact of the insect should it establish in a novel ecosystem. However, divergence time estimates vary among published phylogenetic datasets, making it crucial to understand if and how the choice of phylogeny affects prediction of impact. Here, we tested the robustness of impact prediction to variation in host phylogeny by using insects that feed on conifers and predicting the likelihood of high impact using four different published phylogenies. Our analyses ranked 62 insects that are not established in North America and 47 North American conifer species according to overall risk and vulnerability, respectively. We found that results were robust to the choice of phylogeny. Although published vascular plant phylogenies continue to be refined, our analysis indicates that those differences are not substantial enough to alter the predictions of invader impact. Our results can assist in focusing biosecurity programs for conifer pests and can be more generally applied to nonnative insects and their potential hosts by prioritizing surveillance for those insects most likely to be damaging invaders.

Impact of Stand and Landscape Management on Forest Pest Damage.

One promising approach to mitigate the negative impacts of insect pests in forests is to adapt forestry practices to create ecosystems that are more resistant and resilient to biotic disturbances. At the stand scale, local stand management practices often cause idiosyncratic effects on forest pests depending on the environmental context and the focal pest species. However, increasing tree diversity appears to be a general strategy for reducing pest damage across several forest types. At the landscape scale, increasing forest heterogeneity (e.g., intermixing different forest types and/or age classes) represents a promising frontier for improving forest resistance and resilience and for avoiding large-scale outbreaks. In addition to their greater resilience, heterogeneous forest landscapes frequently support a wide range of ecosystem functions and services. A challenge will be to develop cooperation and coordination among multiple actors at spatial scales that transcend historical practices in forest management.

Discovery Proteomics for COVID-19: Where We Are Now.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus responsible for the pandemic coronavirus disease 2019 (COVID-19), which has had a devastating impact on society. Here, we summarize proteomic research that has helped elucidate hallmark proteins associated with the disease with respect to both short- and long-term diagnosis and prognosis. Additionally, we review the highly variable humoral response associated with COVID-19 and the increased risk of autoimmunity.

Fine roots and mycorrhizal fungi accelerate leaf litter decomposition in a northern hardwood forest regardless of dominant tree mycorrhizal associations.

●Fine roots and mycorrhizal fungi may either stimulate leaf litter decomposition by providing free-living decomposers with root-derived carbon, or may slow decomposition through nutrient competition between mycorrhizal and saprotrophic fungi. ●We reduced the presence of fine roots and their associated mycorrhizal fungi in a northern hardwood forest in New Hampshire, USA by soil trenching. Plots spanned a mycorrhizal gradient from 96% arbuscular mycorrhizal (AM) associations to 100% ectomycorrhizal (ECM)-associated tree basal area. We incubated four species of leaf litter within these plots in areas with reduced access to roots and mycorrhizal fungi and in adjacent areas with intact roots and mycorrhizal fungi. ●Over a period of 608 d, we found that litter decayed more rapidly in the presence of fine roots and mycorrhizal hyphae regardless of the dominant tree mycorrhizal association. Root and mycorrhizal exclusion reduced the activity of acid phosphatase on decomposing litter. ●Our results indicate that both AM- and ECM-associated fine roots stimulate litter decomposition in this system. These findings suggest that the effect of fine roots and mycorrhizal fungi on litter decay in a particular ecosystem likely depends on whether interactions between mycorrhizal roots and saprotrophic fungi are antagonistic or facilitative.

Limited evidence that larger acorns buffer Quercus rubra seedlings from density-dependent biotic stressors.

PREMISE: Plant performance and functional traits vary considerably within species, particularly in response to environmental variation. Plant responses may reflect life-history trade-offs, such as between resource acquisition and resource conservation. Larger seeds may buffer young plants from the negative effects of environmental variation, such as limitations in nutrients or water. However, whether seed size plays a similar role in how plants respond to variation in their biotic environment, including competition and soil microbial communities, remains poorly understood. METHODS: We used a greenhouse experiment to test the interactive effects of intraspecific competition, the origin of the soil microbial community, and seed size on performance and functional traits in Quercus rubra L. seedlings. RESULTS: Intraspecific variation in seedling traits weakly aligned with a resource acquisition-conservation trade-off. Across the wide range of initial acorn mass, competition decreased seedling biomass by about 35%. Competition directly decreased the root mass ratio and indirectly increased specific leaf area and specific root length, via the negative effects on total biomass. In contrast, soil microbial communities had minor effects on seedlings, and we found no differences between plants receiving soil originating from a conspecific adult and plants receiving soil originating from a heterospecific adult. CONCLUSIONS: Competition is a more important driver of intraspecific variation in young Quercus rubra seedling performance and traits, both directly and by delaying ontogenetic development, than soil microbial communities. Seed size is an important predictor of seedling biomass, but a larger seed does not necessarily buffer seedlings from the effects of competition.

Increasing shrub damage by invertebrate herbivores in the warming and drying tundra of West Greenland.

Rapid warming is predicted to increase insect herbivory across the tundra biome, yet how this will impact the community and ecosystem dynamics remains poorly understood. Increasing background invertebrate herbivory could impede Arctic greening, by serving as a top-down control on tundra vegetation. Many tundra ecosystems are also susceptible to severe insect herbivory outbreaks which can have lasting effects on vegetation communities. To explore how tundra-insect herbivore systems respond to warming, we measured shrub traits and foliar herbivory damage at 16 sites along a landscape gradient in western Greenland. Here we show that shrub foliar insect herbivory damage on two dominant deciduous shrubs, Salix glauca and Betula nana, was positively correlated with increasing temperatures throughout the first half of the 2017 growing season. We found that the majority of insect herbivory damage occurred in July, which was outside the period of rapid leaf expansion that occurred throughout most of June. Defoliators caused the most foliar damage in both shrub species. Additionally, insect herbivores removed a larger proportion of B. nana leaf biomass in warmer sites, which is due to a combination of increased foliar herbivory with a coinciding decline in foliar biomass. These results suggest that the effects of rising temperatures on both insect herbivores and host species are important to consider when predicting the trajectory of Arctic tundra shrub expansion.

Quantifying the nature and strength of intraspecific density dependence in Arctic mosquitoes.

Processes that change with density are inherent in all populations, yet quantifying density dependence with empirical data remains a challenge. This is especially true for animals recruiting in patchy landscapes because heterogeneity in habitat quality in combination with habitat choice can obscure patterns expected from density dependence. Mosquitoes (Diptera: Culicidae) typically experience strong density dependence when larvae compete for food, however, effects vary across species and contexts. If populations experience intense intraspecific density-dependent mortality then overcompensation can occur, where the number of survivors declines at high densities producing complex endogenous dynamics. To seek generalizations about density dependence in a widespread species of Arctic mosquito, Aedes nigripes, we combined a laboratory experiment, field observations, and modeling approaches. We evaluated alternative formulations of discrete population models and compared best-performing models from our lab study to larval densities from ponds in western Greenland. Survivorship curves from the lab were the best fit by a Hassell model with compensating density dependence (equivalent to a Beverton-Holt model) where peak recruitment ranged from 8 to 80 mosquitoes per liter depending on resource supply. In contrast, our field data did not show a signal of strong density dependence, suggesting that other processes such as predation may lower realized densities in nature, and that expected patterns may be obscured because larval abundance covaries with resources (cryptic density dependence). Our study emphasizes the importance of covariation between the environment, habitat choice, and density dependence in understanding population dynamics across landscapes, and demonstrates the value of pairing lab and field studies.

The Influence of Water Deficit Stress on the Grapevine Trunk Disease Pathogens Eutypa lata and Diplodia seriata.

The increasing prevalence of the grapevine trunk diseases Eutypa and Botryosphaeria dieback has been attributed, in part, to abiotic stresses imposed on vineyards as production intensifies worldwide. The aim of this study was to evaluate the influence of water deficit irrigation practices on the infection of pruning wounds by Eutypa lata and Diplodia seriata and the subsequent rate of colonization. Two vineyard trials were conducted over two consecutive seasons in South Australia, one in the Riverland with 'Cabernet Sauvignon' with four irrigation treatments (100, 50, 25, and 12.5% of the standard irrigation program) and another in the Barossa Valley with 'Shiraz' on six rootstocks and own roots, either irrigated or not irrigated. According to leaf water potential assessments, vines with reduced irrigation were generally in water deficit and therefore subjected to stress. On the whole, incidence of wound infection and distance of colonization were similar between irrigation treatments for both pathogens, except in the Riverland, where E. lata colonized canes to a greater extent in well-watered vines than those in water deficit. Only vines on rootstock 'Ramsey' in the Barossa Valley had greater extent of colonization by E. lata in the nonirrigated vines. There was no correlation between internal staining and colonization, with both pathogens recovered to nearly 20 cm ahead of the staining. Water deficit did not increase the susceptibility of grapevine pruning wounds to infection or colonization of the subtending tissue by E. lata and D. seriata. In fact, there was evidence of lower susceptibility to colonization by E. lata in vines subjected to severe water deficit.

Northern forest winters have lost cold, snowy conditions that are important for ecosystems and human communities.

Winter is an understudied but key period for the socioecological systems of northeastern North American forests. A growing awareness of the importance of the winter season to forest ecosystems and surrounding communities has inspired several decades of research, both across the northern forest and at other mid- and high-latitude ecosystems around the globe. Despite these efforts, we lack a synthetic understanding of how winter climate change may impact hydrological and biogeochemical processes and the social and economic activities they support. Here, we take advantage of 100 years of meteorological observations across the northern forest region of the northeastern United States and eastern Canada to develop a suite of indicators that enable a cross-cutting understanding of (1) how winter temperatures and snow cover have been changing and (2) how these shifts may impact both ecosystems and surrounding human communities. We show that cold and snow covered conditions have generally decreased over the past 100 years. These trends suggest positive outcomes for tree health as related to reduced fine root mortality and nutrient loss associated with winter frost but negative outcomes as related to the northward advancement and proliferation of forest insect pests. In addition to effects on vegetation, reductions in cold temperatures and snow cover are likely to have negative impacts on the ecology of the northern forest through impacts on water, soils, and wildlife. The overall loss of coldness and snow cover may also have negative consequences for logging and forest products, vector-borne diseases, and human health, recreation, and tourism, and cultural practices, which together represent important social and economic dimensions for the northern forest region. These findings advance our understanding of how our changing winters may transform the socioecological system of a region that has been defined by the contrasting rhythm of the seasons. Our research also identifies a trajectory of change that informs our expectations for the future as the climate continues to warm.

Effect of Rising Temperature on Lyme Disease: Ixodes scapularis Population Dynamics and Borrelia burgdorferi Transmission and Prevalence.

Warmer temperatures are expected to increase the incidence of Lyme disease through enhanced tick maturation rates and a longer season of transmission. In addition, there could be an increased risk of disease export because of infected mobile hosts, usually birds. A temperature-driven seasonal model of Borrelia burgdorferi (Lyme disease) transmission among four host types is constructed as a system of nonlinear ordinary differential equations. The model is developed and parametrized based on a collection of lab and field studies. The model is shown to produce biologically reasonable results for both the tick vector (Ixodes scapularis) and the hosts when compared to a different set of studies. The model is used to predict the response of Lyme disease risk to a mean annual temperature increase, based on current temperature cycles in Hanover, NH. Many of the risk measures suggested by the literature are shown to change with increased mean annual temperature. The most straightforward measure of disease risk is the abundance of infected questing ticks, averaged over a year. Compared to this measure, which is difficult and resource-intensive to track in the field, all other risk measures considered underestimate the rise of risk with rise in mean annual temperature. The measure coming closest was "degree days above zero." Disease prevalence in ticks and hosts showed less increase with rising temperature. Single field measurements at the height of transmission season did not show much change at all with rising temperature.

Anterior segment optical coherence tomography angiography.

We present a novel method to image the vasculature of the anterior segment of the eye using a non-invasive optical coherence tomography angiography (OCTA) system with a modified lens system. This system utilises the Heidelberg Spectralis OCTA and a 3D printed lens mount holding a simple biconvex lens in place to allow capture of images in the anterior segment.

Molecular Methods to Detect and Quantify Botryosphaeriaceae Inocula Associated With Grapevine Dieback in Australia.

Botryosphaeria dieback, caused by species of Botryosphaeriaceae, is an important grapevine trunk disease in Australia. Inocula produced by the pathogens are primarily dispersed by rain splash and wind and infect pruning wounds leading to cankers, dieback, and eventually death of vines. The objective of this study was to develop molecular tools to detect and quantify Botryosphaeriaceae inocula from the environment. These tools are essential for investigating spore dispersal patterns of Botryosphaeriaceae pathogens in Australian vineyards. DNA extraction protocols were evaluated and one modified protocol was found suitable for extracting Botryosphaeriaceae DNA from artificially and naturally inoculated Burkard volumetric spore sampler tapes. Multispecies primers and a hydrolysis probe for quantitative PCR (qPCR) were further developed to detect and quantify Botryosphaeriaceae inocula from environmental samples. Specificity tests showed that the multispecies primers were able to amplify the DNA of 10 Botryosphaeriaceae species (58 isolates) found in Australia while none of the 27 nontarget fungal species (90 isolates) tested were amplified. The qPCR assay was suitable for amplifying purified DNA, synthetic DNA fragments (gBlocks), and mixed DNA from spore trap tapes. The qPCR method developed in this study was shown to be rapid and sensitive in detecting Botryosphaeriaceae inocula from the environment using spore traps.

Latitudinal patterns in temperature-dependent growth rates of a forest pathogen.

Direct effects of temperature on plant pathogens can be crucial to determine the onset and epidemiology of disease. The pinewood nematode Bursaphelenchus xylophilus, the causal agent of the pine wilt disease (PWD), has a wide geographical distribution in Eurasia and East Asia, and local temperatures are considered determinant for the onset of the PWD. However, direct effects of temperature on this pathogen are never considered when forecasting its distribution and impact. In the present study we assessed: 1) at which temperatures is the development of wild populations of the pinewood nematode optimized; 2) if there is niche divergence on different populations from its wide distribution area. For this we studied two populations originated from different latitudes in eastern North America (NA), and used multi-model inference to evaluate the contributions of temperature, diet, and nematode population toward the growth rates of B. xylophilus. Although population origin had some effect on the predictive models, there seems to be niche conservatism, with temperatures of 28-29°C maximizing the growth rates of the pathogen. Thus, the use of the number of days in the summer with temperatures between 25 and 31°C would probably help to improve models forecasting B. xylophilus dispersion and PWD. The present work highlight the importance of considering adaptations to temperatures in forest pathogens with large geographical distributions, when building models forecasting the impact of climate on these organisms.

Long-term species loss and homogenization of moth communities in Central Europe.

As global biodiversity continues to decline steeply, it is becoming increasingly important to understand diversity patterns at local and regional scales. Changes in land use and climate, nitrogen deposition and invasive species are the most important threats to global biodiversity. Because land use changes tend to benefit a few species but impede many, the expected outcome is generally decreasing population sizes, decreasing species richness at local and regional scales, and increasing similarity of species compositions across sites (biotic homogenization). Homogenization can be also driven by invasive species or effects of soil eutrophication propagating to higher trophic levels. In contrast, in the absence of increasing aridity, climate warming is predicted to generally increase abundances and species richness of poikilotherms at local and regional scales. We tested these predictions with data from one of the few existing monitoring programmes on biodiversity in the world dating to the 1960s, where the abundance of 878 species of macro-moths have been measured daily at seven sites across Hungary. Our analyses revealed a dramatic rate of regional species loss and homogenization of community compositions across sites. Species with restricted distribution range, specialized diet or dry grassland habitat were more likely than others to disappear from the community. In global context, the contrasting effects of climate change and land use changes could explain why the predicted enriching effects from climate warming are not always realized.

Nonnative forest insects and pathogens in the United States: Impacts and policy options.

We review and synthesize information on invasions of nonnative forest insects and diseases in the United States, including their ecological and economic impacts, pathways of arrival, distribution within the United States, and policy options for reducing future invasions. Nonnative insects have accumulated in United States forests at a rate of ~2.5 per yr over the last 150 yr. Currently the two major pathways of introduction are importation of live plants and wood packing material such as pallets and crates. Introduced insects and diseases occur in forests and cities throughout the United States, and the problem is particularly severe in the Northeast and Upper Midwest. Nonnative forest pests are the only disturbance agent that has effectively eliminated entire tree species or genera from United States forests within decades. The resulting shift in forest structure and species composition alters ecosystem functions such as productivity, nutrient cycling, and wildlife habitat. In urban and suburban areas, loss of trees from streets, yards, and parks affects aesthetics, property values, shading, stormwater runoff, and human health. The economic damage from nonnative pests is not yet fully known, but is likely in the billions of dollars per year, with the majority of this economic burden borne by municipalities and residential property owners. Current policies for preventing introductions are having positive effects but are insufficient to reduce the influx of pests in the face of burgeoning global trade. Options are available to strengthen the defenses against pest arrival and establishment, including measures taken in the exporting country prior to shipment, measures to ensure clean shipments of plants and wood products, inspections at ports of entry, and post-entry measures such as quarantines, surveillance, and eradication programs. Improved data collection procedures for inspections, greater data accessibility, and better reporting would support better evaluation of policy effectiveness. Lack of additional action places the nation, local municipalities, and property owners at high risk of further damaging and costly invasions. Adopting stronger policies to reduce establishments of new forest insects and diseases would shift the major costs of control to the source and alleviate the economic burden now borne by homeowners and municipalities.

In a warmer Arctic, mosquitoes avoid increased mortality from predators by growing faster.

Climate change is altering environmental temperature, a factor that influences ectothermic organisms by controlling rates of physiological processes. Demographic effects of warming, however, are determined by the expression of these physiological effects through predator-prey and other species interactions. Using field observations and controlled experiments, we measured how increasing temperatures in the Arctic affected development rates and mortality rates (from predation) of immature Arctic mosquitoes in western Greenland. We then developed and parametrized a demographic model to evaluate how temperature affects survival of mosquitoes from the immature to the adult stage. Our studies showed that warming increased development rate of immature mosquitoes (Q10 = 2.8) but also increased daily mortality from increased predation rates by a dytiscid beetle (Q10 = 1.2-1.5). Despite increased daily mortality, the model indicated that faster development and fewer days exposed to predators resulted in an increased probability of mosquito survival to the adult stage. Warming also advanced mosquito phenology, bringing mosquitoes into phenological synchrony with caribou. Increases in biting pests will have negative consequences for caribou and their role as a subsistence resource for local communities. Generalizable frameworks that account for multiple effects of temperature are needed to understand how climate change impacts coupled human-natural systems.

Is climate warming more consequential towards poles? The phenology of Lepidoptera in Finland.

The magnitude and direction of phenological shifts from climate warming could be predictably variable across the planet depending upon the nature of physiological controls on phenology, the thermal sensitivity of the developmental processes and global patterns in the climate warming. We tested this with respect to the flight phenology of adult nocturnal moths (3.33 million captures of 334 species) that were sampled at sites in southern and northern Finland during 1993-2012 (with years 2005-2012 treated as an independent model validation data set). We compared eight competing models of physiological controls on flight phenology to each species and found strong support for thermal controls of phenology in 66% of the species generations. Among species with strong thermal control of phenology in both the south and north, the average development rate was higher in northern vs. southern populations at 10 °C, but about the same at 15 and 20 °C. With a 3 °C increase in temperature (approximating A2 scenario of IPPC for 2090-2099 relative to 1980-1999) these species were predicted to advance their phenology on average by 17 (SE ± 0.3) days in the south vs. 13 (±0.4) days in the north. The higher development rates at low temperatures of poleward populations makes them less sensitive to climate warming, which opposes the tendency for stronger phenological advances in the north from greater increases in temperature.