Understanding ecological systems using knowledge graphs: an application to highly pathogenic avian influenza.

Motivation: Ecological systems are complex. Representing heterogeneous knowledge about ecological systems is a pervasive challenge because data are generated from many subdisciplines, exist in disparate sources, and only capture a subset of interactions underpinning system dynamics. Knowledge graphs (KGs) have been successfully applied to organize heterogeneous data and to predict new linkages in complex systems.

Fruit-frugivore dependencies are important in outbreaks in Sub-Saharan Africa.

Ebolaviruses have the ability to infect a wide variety of species, with many African mammals potentially serving either as primary reservoirs or secondary amplifying hosts. Previous work has shown that frugivorous bats and primates are often associated with spillover and outbreaks. Yet the role that patterns of biodiversity, either of mammalian hosts or of common fruiting species such as (figs, fruit resources used by a wide variety of species), play in driving outbreak risk remains unclear.

Physics-informed deep learning for infectious disease forecasting.

Accurate forecasting of contagious illnesses has become increasingly important to public health policymaking, and better prediction could prevent the loss of millions of lives. To better prepare for future pandemics, it is essential to improve forecasting methods and capabilities. In this work, we propose a new infectious disease forecasting model based on physics-informed neural networks (PINNs), an emerging area of scientific machine learning.

The Mechanisms Underlying the Intergenerational Transmission of Substance Use and Misuse: An Integrated Research Approach.

Substance use and substance use disorders run in families. While it has long been recognized that the etiology of substance use behaviors and disorders involves a combination of genetic and environmental factors, two key questions remain largely unanswered: (1) the intergenerational transmission through which these genetic predispositions are passed from parents to children, and (2) the molecular mechanisms linking genetic variants to substance use behaviors and disorders. This article aims to provide a comprehensive conceptual framework and methodological approach for investigating the intergenerational transmission of substance use behaviors and disorders, by integrating genetic nurture analysis, gene expression imputation, and weighted gene co-expression network analysis.

Photosynthetic temperature responses in leaves and canopies: why temperature optima may disagree at different scales.

Understanding how canopy-scale photosynthesis responds to temperature is of paramount importance for realistic prediction of the likely impact of climate change on forest growth. The effects of temperature on leaf-scale photosynthesis have been extensively documented but data demonstrating the temperature response of canopy-scale photosynthesis are relatively rare, and the mechanisms that determine the response are not well quantified. Here, we compared leaf- and canopy-scale photosynthesis responses to temperature measured in a whole-tree chamber experiment and tested mechanisms that could explain the difference between leaf and crown scale temperature optima for photosynthesis.

Isotopic steady state or non-steady state transpiration? Insights from whole-tree chambers.

Unravelling the complexities of transpiration can be assisted by understanding the oxygen isotope composition of transpired water vapour (δE). It is often assumed that δE is at steady state, thereby mirroring the oxygen isotope composition of source water (δsource), but this assumption has never been tested at the whole-tree scale. This study utilized the unique infrastructure of 12 whole-tree chambers enclosing Eucalyptus parramattensis E.

Challenges of COVID-19 Case Forecasting in the US, 2020-2021.

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub (https://covid19forecasthub.org).

Pushing the envelope: do narrowly and widely distributed Eucalyptus species differ in response to climate warming?

Contemporary climate change will push many tree species into conditions that are outside their current climate envelopes. Using the Eucalyptus genus as a model, we addressed whether species with narrower geographical distributions show constrained ability to cope with warming relative to species with wider distributions, and whether this ability differs among species from tropical and temperate climates. We grew seedlings of widely and narrowly distributed Eucalyptus species from temperate and tropical Australia in a glasshouse under two temperature regimes: the summer temperature at seed origin and +3.

Interconnecting global threats: climate change, biodiversity loss, and infectious diseases.

The concurrent pressures of rising global temperatures, rates and incidence of species decline, and emergence of infectious diseases represent an unprecedented planetary crisis. Intergovernmental reports have drawn focus to the escalating climate and biodiversity crises and the connections between them, but interactions among all three pressures have been largely overlooked. Non-linearities and dampening and reinforcing interactions among pressures make considering interconnections essential to anticipating planetary challenges.

Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations.

Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. Forecasting teams were asked to provide national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one through four weeks ahead for the 2021-22 and 2022-23 influenza seasons. Across both seasons, 26 teams submitted forecasts, with the submitting teams varying between seasons.

A data-driven semi-parametric model of SARS-CoV-2 transmission in the United States.

To support decision-making and policy for managing epidemics of emerging pathogens, we present a model for inference and scenario analysis of SARS-CoV-2 transmission in the USA. The stochastic SEIR-type model includes compartments for latent, asymptomatic, detected and undetected symptomatic individuals, and hospitalized cases, and features realistic interval distributions for presymptomatic and symptomatic periods, time varying rates of case detection, diagnosis, and mortality. The model accounts for the effects on transmission of human mobility using anonymized mobility data collected from cellular devices, and of difficult to quantify environmental and behavioral factors using a latent process.

Bone metastases from chondroblastoma: a rare pattern of metastatic disease in an adult.

Chondroblastoma is a rare benign tumor, typically presenting in the first two decades. Systemic metastases in chondroblastoma are extremely rare and it is the rarity of these metastases which lead the World Health Organisation to re-classify this lesion from "intermediate" to "benign" in its updated classification of bone tumors in 2020. We present an unusual case of a 55 year-old male patient who presented with multiple FDG-avid bone lesions on a background of conventional chondroblastoma of the rib excised at another institution 11-years previously.

S100a9 Protects Against the Effects of Repeated Social Defeat Stress.

Background: Posttraumatic stress disorder, a consequence of psychological trauma, is associated with increased inflammation and an elevated risk of developing comorbid inflammatory diseases. However, the mechanistic link between this mental health disorder and inflammation remains elusive. We previously found that S100a8 and S100a9 messenger RNA, genes that encode the protein calprotectin, were significantly upregulated in T lymphocytes and positively correlated with inflammatory gene expression and the mitochondrial redox environment in these cells.

Disasters collide at the intersection of extreme weather and infectious diseases.

Natural disasters interact to affect the resilience and prosperity of communities and disproportionately affect low income families and communities of colour. However, due to lack of a common theoretical framework, these are rarely quantified. Observing severe weather events (e.

Traits, phylogeny and host cell receptors predict Ebolavirus host status among African mammals.

We explore how animal host traits, phylogenetic identity and cell receptor sequences relate to infection status and mortality from ebolaviruses. We gathered exhaustive databases of mortality from Ebolavirus after exposure and infection status based on PCR and antibody tests. We performed ridge regressions predicting mortality and infection as a function of traits, phylogenetic eigenvectors and separately host receptor sequences.