Country-report pattern corrections of new cases allow accurate 2-week predictions of COVID-19 evolution with the Gompertz model

Accurate short-term predictions of COVID-19 cases with empirical models allow Health Officials to prepare for hospital contingencies in a two-three week window given the delay between case reporting and the admission of patients in a hospital. We investigate the ability of Gompertz-type empiric models to provide accurate prediction up to two and three weeks to give a large window of preparation in case of a surge in virus transmission. We investigate the stability of the prediction and its accuracy using bi-weekly predictions during the last trimester of 2020 and 2021. Using data from 2020, we show that understanding and correcting for the daily reporting structure of cases in the different countries is key to accomplish accurate predictions. Furthermore, we found that filtering out predictions that are highly unstable to changes in the parameters of the model, which are roughly 20%, reduces strongly the number of predictions that are way-off. The method is then tested for robustness with data from 2021. We found that, for this data, only 1-2% of the one-week predictions were off by more than 50%. This increased to 3% for two-week predictions, and only for three-week predictions it reached 10%.

Severity of Omicron Subvariants and Vaccine Impact in Catalonia, Spain

In the current COVID-19 landscape dominated by Omicron subvariants, understanding the timing and efficacy of vaccination against emergent lineages is crucial for planning future vaccination campaigns, yet detailed studies stratified by subvariant, vaccination timing, and age groups are scarce. This retrospective study analyzed COVID-19 cases from December 2021 to January 2023 in Catalonia, Spain, focusing on vulnerable populations affected by variants BA.1, BA.2, BA.5, and BQ.1 and including two national booster campaigns. Our database includes detailed information such as dates of diagnosis, hospitalization and death, last vaccination, and cause of death, among others. We evaluated the impact of vaccination on disease severity by age, variant, and vaccination status, finding that recent vaccination significantly mitigated severity across all Omicron subvariants, although efficacy waned six months post-vaccination, except for BQ.1, which showed more stable levels. Unvaccinated individuals had higher hospitalization and mortality rates. Our results highlight the importance of periodic vaccination to reduce severe outcomes, which are influenced by variant and vaccination timing. Although the seasonality of COVID-19 is uncertain, our analysis suggests the potential benefit of annual vaccination in populations >60 years old, probably in early fall, if COVID-19 eventually exhibits a major peak similar to other respiratory viruses.

Unravelling the role of the mandatory use of face covering masks for the control of SARS-CoV-2 in schools: a quasi-experimental study nested in a population-based cohort in Catalonia (Spain)

OBJECTIVE

To assess the effectiveness of mandatory use of face covering masks (FCMs) in schools during the first term of the 2021-2022 academic year.

DESIGN

A retrospective population-based study.

SETTING

Schools in Catalonia (Spain).

POPULATION

599 314 children aged 3-11 years attending preschool (3-5 years, without FCM mandate) and primary education (6-11 years, with FCM mandate).

STUDY PERIOD

From 13 September to 22 December 2021 (before Omicron variant).

INTERVENTIONS

A quasi-experimental comparison between children in the last grade of preschool (5 years old), as a control group, and children in year 1 of primary education (6 years old), as an interventional group.

MAIN OUTCOME MEASURES

Incidence of SARS-CoV-2, secondary attack rates (SARs) and effective reproductive number (R*).

RESULTS

SARS-CoV-2 incidence was significantly lower in preschool than in primary education, and an increasing trend with age was observed. Six-year-old children showed higher incidence than 5 year olds (3.54% vs 3.1%; OR 1.15 (95% CI 1.08 to 1.22)) and slightly lower but not statistically significant SAR (4.36% vs 4.59%; incidence risk ratio 0.96 (95% CI 0.82 to 1.11)) and R* (0.9 vs 0.93; OR 0.96 (95% CI 0.87 to 1.09)). Results remained consistent using a regression discontinuity design and linear regression extrapolation approaches.

CONCLUSIONS

We found no significant differences in SARS-CoV-2 transmission due to FCM mandates in Catalonian schools. Instead, age was the most important factor in explaining the transmission risk for children attending school.

Low transmission of SARS-CoV-2 derived from children in family clusters: An observational study of family households in the Barcelona Metropolitan Area, Spain

BACKGROUND

Family clusters offer a good opportunity to study viral transmission in a stable setting. We aimed to analyze the specific role of children in transmission of SARS-CoV-2 within households.

METHODS

A prospective, longitudinal, observational study, including children with documented acute SARS-CoV-2 infection attending 22 summer-schools in Barcelona, Spain, was performed. Moreover, other patients and families coming from other school-like environments that voluntarily accessed the study were also studied. A longitudinal follow-up (5 weeks) of the family clusters was conducted to determine whether the children considered to be primary cases were able to transmit the virus to other family members. The household reproduction number (Re*) and the secondary attack rate (SAR) were calculated.

RESULTS

1905 children from the summer schools were screened for SARS-CoV-2 infection and 22 (1.15%) tested positive. Moreover, 32 additional children accessed the study voluntarily. Of these, 37 children and their 26 households were studied completely. In half of the cases (13/26), the primary case was considered to be a child and secondary transmission to other members of the household was observed in 3/13, with a SAR of 14.2% and a Re* of 0.46. Conversely, the SAR of adult primary cases was 72.2% including the kids that gave rise to the contact tracing study, and 61.5% without them, and the estimated Re* was 2.6. In 4/13 of the paediatric primary cases (30.0%), nasopharyngeal PCR was persistently positive > 1 week after diagnosis, and 3/4 of these children infected another family member (p<0.01).

CONCLUSIONS

Children may not be the main drivers of the infection in household transmission clusters in the study population. A prolonged positive PCR could be associated with higher transmissibility.

Age-dependency of the Propagation Rate of Coronavirus Disease 2019 Inside School Bubble Groups in Catalonia, Spain

BACKGROUND

We analyzed contagions of coronavirus disease 2019 inside school bubble groups in Catalonia, Spain, in the presence of strong nonpharmaceutical interventions from September to December 2020. More than 1 million students were organized in bubble groups and monitored and analyzed by the Health and the Educational departments.

METHODS

We had access to 2 data sources, and both were employed for the analysis, one is the Catalan school surveillance system and the other of the educational department. As soon as a positive index case is detected by the health system, isolation is required for all members of the bubble group, in addition to a mandatory proactive systematic screening of each individual. All infected cases are reported. It permits the calculation of the average reproductive number (R*), corresponding to the average number of infected individuals per index case.

RESULTS

We found that propagation inside of the bubble group was small. Among 75% index cases, there was no transmission to other members in the classroom, with an average R* across all ages inside the bubble of R* = 0.4. We found a significant age trend in the secondary attack rates, with the R* going from 0.2 in preschool to 0.6 in high school youth.

CONCLUSIONS

The secondary attack rate depends on the school level and therefore on the age. Super-spreading events (outbreaks of 5 cases or more) in childhood were rare, only occurring in 2.5% of all infections triggered from a pediatric index case.

Stochastic coupled map model of subcellular calcium cycling in cardiac cells

In this study, we analyze a nonlinear map model of intracellular calcium (Ca) and voltage in cardiac cells. In this model, Ca release from the sarcoplasmic reticulum (SR) occurs at spatially distributed dyadic junctions that are diffusively coupled. At these junctions, release occurs with a probability that depends on key variables such as the SR load and the diastolic interval. Using this model, we explore how nonlinearity and stochasticity determine the spatial distribution of Ca release events within a cardiac cell. In particular, we identify a novel synchronization transition, which occurs at rapid pacing rates, in which the global Ca transient transitions from a period 2 response to a period 1 response. In the global period 2 response dyadic junctions fire in unison, on average, on alternate beats, while in the period 1 regime, Ca release at individual dyads is highly irregular. A close examination of the spatial distribution of Ca reveals that in the period 1 regime, the system coarsens into spatially out-of-phase regions with a length scale much smaller than the system size, but larger than the spacing between dyads. We have also explored in detail the coupling to membrane voltage. We study first the case of positive coupling, where a large Ca transient promotes a long action potential duration (APD). Here, the coupling to voltage synchronizes Ca release so that the system exhibits a robust period 2 response that is independent of initial conditions. On the other hand, in the case of negative coupling, where a large Ca transient tends to shorten the APD, we find a multitude of metastable states which consist of complex spatially discordant alternans patterns. Using an analogy to equilibrium statistical mechanics, we show that the spatial patterns observed can be explained by a mapping to the Potts model, with an additional term that accounts for a global coupling of spin states. Using this analogy, we argue that Ca cycling in cardiac cells exhibits complex spatiotemporal patterns that emerge via first or second order phase transitions. These results show that voltage and Ca can interact in order to induce complex subcellular responses, which can potentially lead to heart rhythm disorders.

Publisher's Note: Role of connectivity and fluctuations in the nucleation of calcium waves in cardiac cells [Phys. Rev. E 92, 052715 (2015)]

This corrects the article DOI: 10.1103/PhysRevE.92.052715.

Role of connectivity and fluctuations in the nucleation of calcium waves in cardiac cells

Spontaneous calcium release (SCR) occurs when ion channel fluctuations lead to the nucleation of calcium waves in cardiac cells. This phenomenon is important since it has been implicated as a cause of various cardiac arrhythmias. However, to date, it is not understood what determines the timing and location of spontaneous calcium waves within cells. Here, we analyze a simplified model of SCR in which calcium release is modeled as a stochastic processes on a two-dimensional network of randomly distributed sites. Using this model we identify the essential parameters describing the system and compute the phase diagram. In particular, we identify a critical line which separates pinned and propagating fronts, and show that above this line wave nucleation is governed by fluctuations and the spatial connectivity of calcium release units. Using a mean-field analysis we show that the sites of wave nucleation are predicted by localized eigenvectors of a matrix representing the network connectivity of release sites. This result provides insight on the interplay between connectivity and fluctuations in the genesis of SCR in cardiac myocytes.

Cardiac contraction induces discordant alternans and localized block

In this paper we use a simplified model of cardiac excitation-contraction coupling to study the effect of tissue deformation on the dynamics of alternans, i.e., alternations in the duration of the cardiac action potential, that occur at fast pacing rates and are known to be proarrhythmic. We show that small stretch-activated currents can produce large effects and cause a transition from in-phase to off-phase alternations (i.e., from concordant to discordant alternans) and to conduction blocks. We demonstrate numerically and analytically that this effect is the result of a generic change in the slope of the conduction velocity restitution curve due to electromechanical coupling. Thus, excitation-contraction coupling can potentially play a relevant role in the transition to reentry and fibrillation.

The timing statistics of spontaneous calcium release in cardiac myocytes

A variety of cardiac arrhythmias are initiated by a focal excitation that disrupts the regular beating of the heart. In some cases it is known that these excitations are due to calcium (Ca) release from the sarcoplasmic reticulum (SR) via propagating subcellular Ca waves. However, it is not understood what are the physiological factors that determine the timing of these excitations at both the subcellular and tissue level. In this paper we apply analytic and numerical approaches to determine the timing statistics of spontaneous Ca release (SCR) in a simplified model of a cardiac myocyte. In particular, we compute the mean first passage time (MFPT) to SCR, in the case where SCR is initiated by spontaneous Ca sparks, and demonstrate that this quantity exhibits either an algebraic or exponential dependence on system parameters. Based on this analysis we identify the necessary requirements so that SCR occurs on a time scale comparable to the cardiac cycle. Finally, we study how SCR is synchronized across many cells in cardiac tissue, and identify a quantitative measure that determines the relative timing of SCR in an ensemble of cells. Using this approach we identify the physiological conditions so that cell-to-cell variations in the timing of SCR is small compared to the typical duration of an SCR event. We argue further that under these conditions inward currents due to SCR can summate and generate arrhythmogenic triggered excitations in cardiac tissue.

Identification of intracellular calcium dynamics in stimulated cardiomyocytes

We have developed an automatic method for the analysis and identification of dynamical regimes in intracellular calcium patterns from confocal calcium images. The method allows the identification of different dynamical patterns such as spatially concordant and discordant alternans, irregular behavior or phase-locking regimes such as period doubling or halving. The method can be applied to the analysis of different cardiac pathologies related to anomalies at the cellular level such as ventricular reentrant arrhythmias.

Pattern formation and interface pinch-off in rotating Hele-Shaw flows: a phase-field approach

Viscous fingering dynamics driven by centrifugal forcing is studied for arbitrary viscosity contrast. Theoretical methods, including exact solutions, and numerics based on a phase-field approach are used. Both confirm that pinch-off singularities in patterns originated from the centrifugally driven instability may occur spontaneously and be inherent to the two-dimensional Hele-Shaw dynamics. They are systematically more frequent for lower viscosity contrasts consistently with experimental evidence. The analytical insights provide an interpretation of this fact in terms of the asymptotic matching of the different regions of the fingering patterns. The phase-field numerical scheme is shown to be particularly adequate to elucidate the existence of finite-time singularities through the dependence of the singularity time on the interface thickness, in particular for varying viscosity contrast.

Pinch-off singularities in rotating Hele-Shaw flows at high viscosity contrast

We study the evolution of a family of dumbbell-shaped liquid patches surrounded by air inside a rotating Hele-Shaw cell with lubrication methods and numerical simulations. Depending on initial conditions, the dumbbell either stretches to infinity, pinches off at the neck to form a droplet, or collects into a circular drop at the center of rotation. Whether or not pinch-off occurs results from a subtle interplay between centrifugal and capillary forces. In particular, rotation may delay or even prevent pinch-off from occurring owing to stretching and smoothing of the fluid neck. However, frequently rotation may have the opposite effect leading to pinch-off where the relaxation toward a circular drop would be observed in an ordinary Hele-Shaw cell.

Global coupling in excitable media provides a simplified description of mechanoelectrical feedback in cardiac tissue

Cardiac mechanoelectric feedback can play an important role in different heart pathologies. In this paper, we show that mechanoelectric models which describe both the electric propagation and the mechanic contraction of cardiac tissue naturally lead to close systems of equations with global coupling among the variables. This point is exemplified using the Nash-Panfilov model, which reduces to a FitzHugh-Nagumo-type equation with global coupling in the linear elastic regime. We explain the appearance of self-oscillatory regimes in terms of the system nullclines and describe the different dynamical attractors. Finally, we study their basin of attraction in terms of the system size and the strength of the stretch-induced currents.

Relevance of dynamic wetting in viscous fingering patterns

We demonstrate that wetting effects at moving contact lines have a strong impact in viscous fingering patterns. Experiments in a rotating Hele-Shaw (HS) cell, dry or prewetted, show consistent morphological differences. When the wetting fluid invades a dry region, contact angle dynamics yield a kinetic contribution to the interface pressure drop that scales with capillary number as Ca(2/3) but is significantly larger than the Park-Homsy kinetic correction. Numerical results are in very good agreement with experiments and show that standard HS equations work best for prewetted cells.

Hierarchical structures induce long-range dynamical correlations in written texts

Thoughts and ideas are multidimensional and often concurrent, yet they can be expressed surprisingly well sequentially by the translation into language. This reduction of dimensions occurs naturally but requires memory and necessitates the existence of correlations, e.g., in written text. However, correlations in word appearance decay quickly, while previous observations of long-range correlations using random walk approaches yield little insight on memory or on semantic context. Instead, we study combinations of words that a reader is exposed to within a "window of attention," spanning about 100 words. We define a vector space of such word combinations by looking at words that co-occur within the window of attention, and analyze its structure. Singular value decomposition of the co-occurrence matrix identifies a basis whose vectors correspond to specific topics, or "concepts" that are relevant to the text. As the reader follows a text, the "vector of attention" traces out a trajectory of directions in this "concept space." We find that memory of the direction is retained over long times, forming power-law correlations. The appearance of power laws hints at the existence of an underlying hierarchical network. Indeed, imposing a hierarchy similar to that defined by volumes, chapters, paragraphs, etc. succeeds in creating correlations in a surrogate random text that are identical to those of the original text. We conclude that hierarchical structures in text serve to create long-range correlations, and use the reader's memory in reenacting some of the multidimensionality of the thoughts being expressed.

Molecular model of the contractile ring

We present a model for the actin contractile ring of adherent animal cells. The model suggests that the actin concentration within the ring and consequently the power that the ring exerts both increase during contraction. We demonstrate the crucial role of actin polymerization and depolymerization throughout cytokinesis, and the dominance of viscous dissipation in the dynamics. The physical origin of two phases in cytokinesis dynamics ("biphasic cytokinesis") follows from a limitation on the actin density. The model is consistent with a wide range of measurements of the midzone of dividing animal cells.

Nonlinear Saffman-Taylor instability

We show, both theoretically and experimentally, that the interface between two viscous fluids in a Hele-Shaw cell can be nonlinearly unstable before the Saffman-Taylor linear instability point is reached. We identify the family of exact elastica solutions [Nye et al., Eur. J. Phys. 5, 73 (1984)]] as the unstable branch of the corresponding subcritical bifurcation which ends up at a topological singularity defined by interface pinchoff. We devise an experimental procedure to prepare arbitrary initial conditions in a Hele-Shaw cell. This is used to test the proposed bifurcation scenario and quantitatively asses its practical relevance.

Systematic weakly nonlinear analysis of radial viscous fingering

We present a weakly nonlinear analysis of the interface dynamics in a radial Hele-Shaw cell driven by both injection and rotation. We extend the systematic expansion introduced in [E. Alvarez-Lacalle et al., Phys. Rev. E 64, 016302 (2001)] to the radial geometry, and compute explicitly the first nonlinear contributions. We also find the necessary and sufficient condition for the uniform convergence of the nonlinear expansion. Within this region of convergence, the analytical predictions at low orders are compared satisfactorily to exact solutions and numerical integration of the problem. This is particularly remarkable in configurations (with no counterpart in the channel geometry) for which the interplay between injection and rotation allows that condition to be satisfied at all times. In the case of the purely centrifugal forcing we demonstrate that nonlinear couplings make the interface more unstable for lower viscosity contrast between the fluids.

Systematic weakly nonlinear analysis of interfacial instabilities in Hele-Shaw flows

We develop a systematic method to derive all orders of mode couplings in a weakly nonlinear approach to the dynamics of the interface between two immiscible viscous fluids in a Hele-Shaw cell. The method is completely general: it applies to arbitrary geometry and driving. Here we apply it to the channel geometry driven by gravity and pressure. The finite radius of convergence of the mode-coupling expansion is found. Calculation up to third-order couplings is done, which is necessary to account for the time-dependent Saffman-Taylor finger solution and the case of zero viscosity contrast. The explicit results provide relevant analytical information about the role that the viscosity contrast and the surface tension play in the dynamics of the system. We finally check the quantitative validity of different orders of approximation and a resummation scheme against a physically relevant, exact time-dependent solution. The agreement between the low-order approximations and the exact solution is excellent within the radius of convergence, and is even reasonably good beyond this radius.