Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern: a retrospective analysis.

The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants.

Modelling seasonality of Lassa fever incidences and vector dynamics in Nigeria.

Lassa fever (Lf) is a viral haemorrhagic disease endemic to West Africa and is caused by the Lassa mammarenavirus. The rodent Mastomys natalensis serves as the primary reservoir and its ecology and behaviour have been linked to the distinct spatial and temporal patterns in the incidence of Lf. Nigeria has experienced an unprecedented epidemic that lasted from January until April of 2018, which has been followed by subsequent epidemics of Lf in the same period every year since.

Rolling and Sliding Modes of Nanodroplet Spreading: Molecular Simulations and a Continuum Approach.

Molecular simulations discover a new mode of dynamic wetting that manifests itself in the very earliest stages of spreading, after a droplet contacts a solid. The observed mode is a "rolling" type of motion, characterized by a contact angle lower than the classically assumed value of 180°, and precedes the conventional "sliding" mode of spreading. This motivates the development of a novel continuum framework that captures all modes of motion, allows the dominant physical mechanisms to be understood, and permits the study of larger droplets.

Modeling Leidenfrost Levitation of Soft Elastic Solids.

The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge.

Efficient approximation of cardiac mechanics through reduced-order modeling with deep learning-based operator approximation.

Reducing the computational time required by high-fidelity, full-order models (FOMs) for the solution of problems in cardiac mechanics is crucial to allow the translation of patient-specific simulations into clinical practice. Indeed, while FOMs, such as those based on the finite element method, provide valuable information on the cardiac mechanical function, accurate numerical results can be obtained at the price of very fine spatio-temporal discretizations. As a matter of fact, simulating even just a few heartbeats can require up to hours of wall time on high-performance computing architectures.

A new flow-based design for double-lumen needles.

Oocyte retrieval forms a crucial part of in vitro fertilisation treatment and its ultimate outcome. Standard double-lumen needles, which include a sequence of aspiration and flushing steps, are characterised by a similar success rate to single-lumen needles, despite their increased cost. A novel hydrodynamics-based needle called the OxIVF needle is proposed here, which is geared towards the generation of an internal flow field within the full follicular volume via laterally, rather than frontally, oriented flushing, leading to successful retrievals with no additional stress on the oocyte.

Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study.

In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multiscale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), accounting for within-host viral dynamics. Compared to population-level models previously used to estimate outbreak risks, our approach enables more detailed analysis of how the risk can be mitigated through pre-emptive interventions such as antigen testing.

Orienteering with One Endomorphism.

In supersingular isogeny-based cryptography, the path-finding problem reduces to the endomorphism ring problem. Can path-finding be reduced to knowing just one endomorphism? It is known that a small degree endomorphism enables polynomial-time path-finding and endomorphism ring computation (in: Love and Boneh, ANTS XIV-Proceedings of the Fourteenth Algorithmic Number Theory Symposium, volume 4 of Open Book Ser. Math.

Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists.

Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the [Formula: see text]-opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives.

Reduced basis surrogates for quantum spin systems based on tensor networks.

Within the reduced basis methods approach, an effective low-dimensional subspace of a quantum many-body Hilbert space is constructed in order to investigate, e.g., the ground-state phase diagram.

Generalized Cuts of Feynman Integrals in Parameter Space.

We propose a construction of generalized cuts of Feynman integrals as an operation on the domain of the Feynman parametric integral. A set of on-shell conditions removes the corresponding boundary components of the integration domain, in favor of including a boundary component from the second Symanzik polynomial. Hence integration domains are full-dimensional spaces with finite volumes, rather than being localized around poles.

Incorporating heterogeneity in farmer disease control behaviour into a livestock disease transmission model.

Human behaviour is critical to effective responses to livestock disease outbreaks, especially with respect to vaccination uptake. Traditionally, mathematical models used to inform this behaviour have not taken heterogeneity in farmer behaviour into account. We address this by exploring how heterogeneity in farmers vaccination behaviour can be incorporated to inform mathematical models.

Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach.

African horse sickness is an equine orbivirus transmitted by Culicoides Latreille biting midges. In the last 80 years, it has caused several devastating outbreaks in the equine population in Europe, the Far and Middle East, North Africa, South-East Asia, and sub-Saharan Africa. The disease is endemic in South Africa; however, a unique control area has been set up in the Western Cape where increased surveillance and control measures have been put in place.

A detailed mathematical model of the human atrial cardiomyocyte: integration of electrophysiology and cardiomechanics.

Mechano-electric regulations (MER) play an important role in the maintenance of cardiac performance. Mechano-calcium and mechano-electric feedback (MCF and MEF) pathways adjust the cardiomyocyte contractile force according to mechanical perturbations and affects electro-mechanical coupling. MER integrates all these regulations in one unit resulting in a complex phenomenon.

Effectiveness of testing, contact tracing and isolation interventions among the general population on reducing transmission of SARS-CoV-2: a systematic review.

We conducted a systematic literature review of general population testing, contact tracing, case isolation and contact quarantine interventions to assess their effectiveness in reducing SARS-CoV-2 transmission, as implemented in real-world settings. We designed a broad search strategy and aimed to identify peer-reviewed studies of any design provided there was a quantitative measure of effectiveness on a transmission outcome. Studies that assessed the effect of testing or diagnosis on disease outcomes via treatment, but did not assess a transmission outcome, were not included.

A modelling analysis of a new multi-stage pathway for classifying achievement of public health milestones for leprosy.

Several countries have come close to eliminating leprosy, but leprosy cases continue to be detected at low levels. Due to the long, highly variable delay from infection to detection, the relationship between observed cases and transmission is uncertain. The World Health Organization's new technical guidance provides a path for countries to reach elimination.

Bayesian inference of polymerase dynamics over the exclusion process.

Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference over a paradigmatic mechanistic model of non-equilibrium statistical physics, i.e.

Epidemiological impacts of attenuated African swine fever virus circulating in wild boar populations.

African swine fever virus (ASFV) genotype II has been present in wild boar in the European Union since 2014. Control measures have reduced the incidence of the ASF, but highly virulent as well as attenuated ASFV strains continue to circulate. We present the intraherd epidemiological parameters of low and highly virulent ASFV in wild boar from experimental data, and for the first time, evaluate the impact of attenuated strain circulation through unique deterministic compartmental model simulations under various potential scenarios and hypotheses.

Towards the sustainable elimination of gambiense human African trypanosomiasis in Côte d'Ivoire using an integrated approach.

Background: Human African trypanosomiasis is a parasitic disease caused by trypanosomes among which Trypanosoma brucei gambiense is responsible for a chronic form (gHAT) in West and Central Africa. Its elimination as a public health problem (EPHP) was targeted for 2020. Côte d'Ivoire was one of the first countries to be validated by WHO in 2020 and this was particularly challenging as the country still reported around a hundred cases a year in the early 2000s.

Health economic evaluation of strategies to eliminate gambiense human African trypanosomiasis in the Mandoul disease focus of Chad.

Human African trypanosomiasis, caused by the gambiense subspecies of Trypanosoma brucei (gHAT), is a deadly parasitic disease transmitted by tsetse. Partners worldwide have stepped up efforts to eliminate the disease, and the Chadian government has focused on the previously high-prevalence setting of Mandoul. In this study, we evaluate the economic efficiency of the intensified strategy that was put in place in 2014 aimed at interrupting the transmission of gHAT, and we make recommendations on the best way forward based on both epidemiological projections and cost-effectiveness.

A time-dependent Poisson-Gamma model for recruitment forecasting in multicenter studies.

Forecasting recruitments is a key component of the monitoring phase of multicenter studies. One of the most popular techniques in this field is the Poisson-Gamma recruitment model, a Bayesian technique built on a doubly stochastic Poisson process. This approach is based on the modeling of enrollments as a Poisson process where the recruitment rates are assumed to be constant over time and to follow a common Gamma prior distribution.

Discrete time model of sexual systems.

Small factors are the biggest contributors to the biggest changes in an ecosystem which may lead to its demise. Simple things such as tweaking the humidity or tampering with the temperature can be the downfall of the habitants and the ecosystem itself. These changes can be observed right now with the consistent temperature increase on Earth along with the slew of issues that come with global warming.

Non-intersecting Path Constructions for TASEP with Inhomogeneous Rates and the KPZ Fixed Point.

We consider a discrete-time TASEP, where each particle jumps according to Bernoulli random variables with particle-dependent and time-inhomogeneous parameters. We use the combinatorics of the Robinson-Schensted-Knuth correspondence and certain intertwining relations to express the transition kernel of this interacting particle system in terms of ensembles of weighted, non-intersecting lattice paths and, consequently, as a marginal of a determinantal point process. We next express the joint distribution of the particle positions as a Fredholm determinant, whose correlation kernel is given in terms of a boundary-value problem for a discrete heat equation.