Community structure determines the predictability of population collapse.

Early warning signals (EWS) are phenomenological tools that have been proposed as predictors of the collapse of biological systems. Although a growing body of work has shown the utility of EWS based on either statistics derived from abundance data or shifts in phenotypic traits such as body size, so far this work has largely focused on single species populations. However, to predict reliably the future state of ecological systems, which inherently could consist of multiple species, understanding how reliable such signals are in a community context is critical. Here, reconciling quantitative trait evolution and Lotka-Volterra equations, which allow us to track both abundance and mean traits, we simulate the collapse of populations embedded in mutualistic and multi-trophic predator-prey communities. Using these simulations and warning signals derived from both population- and community-level data, we showed the utility of abundance-based EWS, as well as metrics derived from stability-landscape theory (e.g. width and depth of the basin of attraction), were fundamentally linked. Thus, the depth and width of such stability-landscape curves could be used to identify which species should exhibit the strongest EWS of collapse. The probability a species displays both trait and abundance-based EWS was dependent on its position in a community, with some species able to act as indicator species. In addition, our results also demonstrated that in general trait-based EWS were less reliable in comparison with abundance-based EWS in forecasting species collapses in our simulated communities. Furthermore, community-level abundance-based EWS were fairly reliable in comparison with their species-level counterparts in forecasting species-level collapses. Our study suggests a holistic framework that combines abundance-based EWS and metrics derived from stability-landscape theory that may help in forecasting species loss in a community context.

Longitudinal Changes of COVID-19 Symptoms in Social Media: Observational Study.

BACKGROUND: In December 2019, the COVID-19 outbreak started in China and rapidly spread around the world. Many studies have been conducted to understand the clinical characteristics of COVID-19, and recently postinfection sequelae of this disease have begun to be investigated. However, there is little consensus on the longitudinal changes of lasting physical or psychological symptoms from prior COVID-19 infection. OBJECTIVE: This study aims to investigate and analyze public social media data from Reddit to understand the longitudinal impact of COVID-19 symptoms before and after recovery from COVID-19. METHODS: We collected 22,890 Reddit posts that were generated by 14,401 authors from March 14 to December 16, 2020. Using active learning and intensive manual inspection, 292 (2.03%) active authors, who were infected by COVID-19 and frequently reported disease progress on Reddit, along with their 2213 (9.67%) longitudinal posts, were identified. Machine learning tools to extract biomedical information were applied to identify COVID-19 symptoms mentioned in the Reddit posts. We then examined longitudinal changes in individual physiological and psychological characteristics before and after recovery from COVID-19 infection. RESULTS: In total, 58 physiological and 3 psychological symptoms were identified in social media before and after recovery from COVID-19 infection. From the analyses, we found that symptoms of patients with COVID-19 lasted 2.5 months. On average, symptoms appeared around a month before recovery and remained for 1.5 months after recovery. Well-known COVID-19 symptoms, such as fever, cough, and chest congestion, appeared relatively earlier in patient journeys and were frequently observed before recovery from COVID-19. Meanwhile, mental discomfort or distress, such as brain fog or stress, fatigue, and manifestations on toes or fingers, were frequently mentioned after recovery and remained as intermediate- and longer-term sequelae. CONCLUSIONS: In this study, we showed the dynamic changes in COVID-19 symptoms during the infection and recovery phases of the disease. Our findings suggest the feasibility of using social media data for investigating disease states and understanding the evolution of the physiological and psychological characteristics of COVID-19 infection over time.

The impact of individual variation on abrupt collapses in mutualistic networks.

Individual variation is central to species involved in complex interactions with others in an ecological system. Such ecological systems could exhibit tipping points in response to changes in the environment, consequently leading to abrupt transitions to alternative, often less desirable states. However, little is known about how individual trait variation could influence the timing and occurrence of abrupt transitions. Using 101 empirical mutualistic networks, I model the eco-evolutionary dynamics of such networks in response to gradual changes in strength of co-evolutionary interactions. Results indicated that individual variation facilitates the timing of transition in such networks, albeit slightly. In addition, individual variation significantly increases the occurrence of large abrupt transitions. Furthermore, topological network features also positively influence the occurrence of such abrupt transitions. These findings argue for understanding tipping points using an eco-evolutionary perspective to better forecast abrupt transitions in ecological systems.

Identification of Risk Factors and Symptoms of COVID-19: Analysis of Biomedical Literature and Social Media Data.

BACKGROUND: In December 2019, the COVID-19 outbreak started in China and rapidly spread around the world. Lack of a vaccine or optimized intervention raised the importance of characterizing risk factors and symptoms for the early identification and successful treatment of patients with COVID-19. OBJECTIVE: This study aims to investigate and analyze biomedical literature and public social media data to understand the association of risk factors and symptoms with the various outcomes observed in patients with COVID-19. METHODS: Through semantic analysis, we collected 45 retrospective cohort studies, which evaluated 303 clinical and demographic variables across 13 different outcomes of patients with COVID-19, and 84,140 Twitter posts from 1036 COVID-19-positive users. Machine learning tools to extract biomedical information were introduced to identify mentions of uncommon or novel symptoms in tweets. We then examined and compared two data sets to expand our landscape of risk factors and symptoms related to COVID-19. RESULTS: From the biomedical literature, approximately 90% of clinical and demographic variables showed inconsistent associations with COVID-19 outcomes. Consensus analysis identified 72 risk factors that were specifically associated with individual outcomes. From the social media data, 51 symptoms were characterized and analyzed. By comparing social media data with biomedical literature, we identified 25 novel symptoms that were specifically mentioned in tweets but have been not previously well characterized. Furthermore, there were certain combinations of symptoms that were frequently mentioned together in social media. CONCLUSIONS: Identified outcome-specific risk factors, symptoms, and combinations of symptoms may serve as surrogate indicators to identify patients with COVID-19 and predict their clinical outcomes in order to provide appropriate treatments.

Predicting Glycaemia in Type 1 Diabetes Patients: Experiments in Feature Engineering and Data Imputation.

Patients with type 1 diabetes manually regulate blood glucose concentration by adjusting insulin dosage in response to factors such as carbohydrate intake and exercise intensity. Automated near-term prediction of blood glucose concentration is essential to prevent hyper- and hypoglycaemic events in type 1 diabetes patients and to improve control of blood glucose levels by physicians and patients. The imperfect nature of patient monitoring introduces missing values into all variables that play important roles to predict blood glucose level, necessitating data imputation. In this paper, we investigated the importance of variables and explored various feature engineering methods to predict blood glucose level. Next, we extended our work by developing a new empirical imputation method and investigating the predictive accuracy achieved under different methods to impute missing data. Also, we examined the influence of past signal values on the prediction of blood glucose levels. We reported the relative performance of predictive models in different testing scenarios and different imputation methods. Finally, we found an optimal combination of data imputation methods and built an ensemble model for the reliable prediction of blood glucose levels on a 30-minute horizon.

Eco-evolutionary processes underlying early warning signals of population declines.

Environmental change can impact the stability of ecological systems and cause rapid declines in populations. Abundance-based early warning signals have been shown to precede such declines, but detection prior to wild population collapses has had limited success, leading to the development of warning signals based on shifts in distribution of fitness-related traits such as body size. The dynamics of population abundances and traits in response to external environmental perturbations are controlled by a range of underlying factors such as reproductive rate, genetic variation and plasticity. However, it remains unknown how such ecological and evolutionary factors affect the stability landscape of populations and the detectability of abundance and trait-based early warning signals. Here, we apply a trait-based demographic approach and investigate both trait and population dynamics in response to gradual and increasing changes in the environment. We explore a range of ecological and evolutionary constraints under which stability of a population may be affected. We show both analytically and with simulations that strength of abundance- and trait-based warning signals are affected by ecological and evolutionary factors. Finally, we show that combining trait- and abundance-based information improves our ability to predict population declines. Our study suggests that the inclusion of trait dynamic information alongside generic warning signals should provide more accurate forecasts of the future state of biological systems.

When Do Shifts in Trait Dynamics Precede Population Declines?

Predicting population responses to environmental change is an ongoing challenge in ecology. Studies investigating the links between fitness-related phenotypic traits and demography have shown that trait dynamic responses to environmental change can sometimes precede population dynamic responses and thus can be used as an early warning signal. However, it is still unknown under which ecological and evolutionary circumstances shifts in fitness-related traits can precede population responses to environmental perturbation. Here, we take a trait-based demographic approach and investigate both trait and population dynamics in a density-regulated population in response to a gradual change in the environment. We explore the ecological and evolutionary constraints under which shifts in fitness-related traits precede a decline in population size. We show both analytically and with experimental data that under medium to slow rates of environmental change, shifts in a trait value can precede population decline. We further show the positive influence of environmental predictability, net reproductive rate, plasticity, and genetic variation on shifts in trait dynamics preceding potential population declines. These results still hold under nonconstant genetic variation and environmental stochasticity. Our study highlights ecological and evolutionary circumstances under which a fitness-related trait can be used as an early warning signal of an impending population decline.

Community and species-specific responses of plant traits to 23 years of experimental warming across subarctic tundra plant communities.

To improve understanding of how global warming may affect competitive interactions among plants, information on the responses of plant functional traits across species to long-term warming is needed. Here we report the effect of 23 years of experimental warming on plant traits across four different alpine subarctic plant communities: tussock tundra, Dryas heath, dry heath and wet meadow. Open-top chambers (OTCs) were used to passively warm the vegetation by 1.5-3 °C. Changes in leaf width, leaf length and plant height of 22 vascular plant species were measured. Long-term warming significantly affected all plant traits. Overall, plant species were taller, with longer and wider leaves, compared with control plots, indicating an increase in biomass in warmed plots, with 13 species having significant increases in at least one trait and only three species having negative responses. The response varied among species and plant community in which the species was sampled, indicating community-warming interactions. Thus, plant trait responses are both species- and community-specific. Importantly, we show that there is likely to be great variation between plant species in their ability to maintain positive growth responses over the longer term, which might cause shifts in their relative competitive ability.