Tim Bayne, Anil K. Seth, Marcello Massimini, Joshua Shepherd, Axel Cleeremans, Stephen M. Fleming, Rafael Malach, Jason B. Mattingley, David K. Menon, Adrian M. Owen, Megan A.K. Peters, Adeel Razi, Liad Mudrik

Trends in Cognitive Science

Which systems/organisms are conscious? New tests for consciousness (‘C-tests’) are
urgently needed. There is persisting uncertainty about when consciousness arises in
human development, when it is lost due to neurological disorders and brain injury,
and how it is distributed in nonhuman species. This need is amplified by recent and
rapid developments in artificial intelligence (AI), neural organoids, and xenobot
technology. Although a number of C-tests have been proposed in recent years, most
are of limited use, and currently we have no C-tests for many of the populations in
which they are most urgently needed. Here, we identify challenges facing any attempt
to develop C-tests, propose a multidimensional classification of such tests, and identify
strategies that might be used to validate them.

Read the full article at: www.cell.com

Matteo Chinazzi, Jessica T. Davis, Ana Pastore y Piontti, Kunpeng Mu, Nicolò Gozzi, Marco Ajelli, Nicola Perra, Alessandro Vespignani

Epidemics

The Scenario Modeling Hub (SMH) initiative provides projections of potential epidemic scenarios in the United States (US) by using a multi-model approach. Our contribution to the SMH is generated by a multiscale model that combines the global epidemic metapopulation modeling approach (GLEAM) with a local epidemic and mobility model of the US (LEAM-US), first introduced here. The LEAM-US model consists of 3142 subpopulations each representing a single county across the 50 US states and the District of Columbia, enabling us to project state and national trajectories of COVID-19 cases, hospitalizations, and deaths under different epidemic scenarios. The model is age-structured, and multi-strain. It integrates data on vaccine administration, human mobility, and non-pharmaceutical interventions. The model contributed to all 17 rounds of the SMH, and allows for the mechanistic characterization of the spatio-temporal heterogeneities observed during the COVID-19 pandemic. Here we describe the mathematical and computational structure underpinning our model, and present as a case study the results concerning the emergence of the SARS-CoV-2 Alpha variant (lineage designation B.1.1.7). Our findings reveal considerable spatial and temporal heterogeneity in the introduction and diffusion of the Alpha variant, both at the level of individual states and combined statistical areas, as it competes against the ancestral lineage. We discuss the key factors driving the time required for the Alpha variant to rise to dominance within a population, and quantify the significant impact that the emergence of the Alpha variant had on the effective reproduction number at the state level. Overall, we show that our multiscale modeling approach is able to capture the complexity and heterogeneity of the COVID-19 pandemic response in the US.

Read the full article at: www.sciencedirect.com

Thomas P. Wytock and Adilson E. Motter

PNAS 121 (11) e2312942121

The lack of genome-wide mathematical models for the gene regulatory network complicates the application of control theory to manipulate cell behavior in humans. We address this challenge by developing a transfer learning approach that leverages genome-wide transcriptomic profiles to characterize cell type attractors and perturbation responses. These responses are used to predict a combinatorial perturbation that minimizes the transcriptional difference between an initial and target cell type, bringing the regulatory network to the target cell type basin of attraction. We anticipate that this approach will enable the rapid identification of potential targets for treatment of complex diseases, while also providing insight into how the dynamics of gene regulatory networks affect phenotype.
Read the full article at: www.pnas.org