Measuring dynamical systems on directed hypergraphs.

Networks and graphs provide a simple but effective model to a vast set of systems in which building blocks interact throughout pairwise interactions. Unfortunately, such models fail to describe all those systems in which building blocks interact at a higher order. Higher-order graphs provide us the right tools for the task, but introduce a higher computing complexity due to the interaction order.

Assessing the influence of French vaccine critics during the two first years of the COVID-19 pandemic.

When the threat of COVID-19 became widely acknowledged, many hoped that this pandemic would squash "the anti-vaccine movement". However, when vaccines started arriving in rich countries at the end of 2020, it appeared that vaccine hesitancy might be an issue even in the context of this major pandemic. Does it mean that the mobilization of vaccine-critical activists on social media is one of the main causes of this reticence to vaccinate against COVID-19? In this paper, we wish to contribute to current work on vaccine hesitancy during the COVID-19 pandemic by looking at one of the many mechanisms which can cause reticence towards vaccines: the capacity of vaccine-critical activists to influence a wider public on social media.

Data-driven identification of communities with high levels of tuberculosis infection in the Democratic Republic of Congo.

When access to diagnosis and treatment of tuberculosis is disrupted by poverty or unequal access to health services, marginalized communities not only endorse the burden of preventable deaths, but also suffer from the dramatic consequences of a disease which impacts one's ability to access education and minimal financial incomes. Unfortunately, these pockets are often left unrecognized in the flow of data collected in national tuberculosis reports, as localized hotspots are diluted in aggregated reports focusing on notified cases. Such system is therefore profoundly inadequate to identify these marginalized groups, which urgently require adapted interventions.

State Aggregations in Markov Chains and Block Models of Networks.

We consider state-aggregation schemes for Markov chains from an information-theoretic perspective. Specifically, we consider aggregating the states of a Markov chain such that the mutual information of the aggregated states separated by T time steps is maximized. We show that for T=1 this recovers the maximum-likelihood estimator of the degree-corrected stochastic block model as a particular case, which enables us to explain certain features of the likelihood landscape of this generative network model from a dynamical lens.

Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: an observational study.

Background: Global roll-out of rapid molecular assays is revolutionising the diagnosis of rifampicin resistance, predictive of multidrug-resistance, in tuberculosis. However, 30% of the multidrug-resistant (MDR) strains in an eSwatini study harboured the Ile491Phe mutation in the rpoB gene, which is associated with poor rifampicin-based treatment outcomes but is missed by commercial molecular assays or scored as susceptible by phenotypic drug-susceptibility testing deployed in South Africa. We evaluated the presence of Ile491Phe among South African tuberculosis isolates reported as isoniazid-monoresistant according to current national testing algorithms.

Mapping the Topography of a Protein Energy Landscape.

Protein energy landscapes are highly complex, yet the vast majority of states within them tend to be invisible to experimentalists. Here, using site-directed mutagenesis and exploiting the simplicity of tandem-repeat protein structures, we delineate a network of these states and the routes between them. We show that our target, gankyrin, a 226-residue 7-ankyrin-repeat protein, can access two alternative (un)folding pathways.

Quantum transport enhancement by time-reversal symmetry breaking.

Quantum mechanics still provides new unexpected effects when considering the transport of energy and information. Models of continuous time quantum walks, which implicitly use time-reversal symmetric Hamiltonians, have been intensely used to investigate the effectiveness of transport. Here we show how breaking time-reversal symmetry of the unitary dynamics in this model can enable directional control, enhancement, and suppression of quantum transport.

MS/MS spectra interpretation as a statistical-mechanics problem.

We describe a new method for peptide sequencing based on the mapping of the interpretation of tandem mass spectra onto the analysis of the equilibrium distribution of a suitably defined physical model, whose variables describe the positions of the fragmentation sites along a discrete mass index. The model is governed by a potential energy function that, at present, we derive ad hoc from the distribution of peaks in a data set of experimental spectra. The statistical-physics perspective prompts for a consistent and unified approach to de novo and database-search methods, which is a distinctive feature of this approach over alternative ones: the characterization of the ground state of the model allows the de novo identification of the precursor peptide; the study of the thermodynamic variables as a function of the (fictitious) temperature gives insight on the quality of the prediction, while the probability profiles at nonzero temperature reveal, on one hand, which fragments are more reliably predicted.

Analysis of the equilibrium and kinetics of the ankyrin repeat protein myotrophin.

We apply the Wako-Saito-Muñoz-Eaton model to the study of myotrophin, a small ankyrin repeat protein, whose folding equilibrium and kinetics have been recently characterized experimentally. The model, which is a native-centric with binary variables, provides a finer microscopic detail than the Ising model that has been recently applied to some different repeat proteins, while being still amenable for an exact solution. In partial agreement with the experiments, our results reveal a weakly three-state equilibrium and a two-state-like kinetics of the wild-type protein despite the presence of a nontrivial free-energy profile.