Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland

In this study we describe a simulation platform used to create a virtual society of Poland, with a particular emphasis on contact patterns arising from daily commuting to schools or workplaces. In order to reproduce the map of contacts, we are using a geo-referenced Agent Based Model. Within this framework, we propose a set of different stochastic algorithms, utilizing available aggregated census data. Based on this model system, we present selected statistical analysis, such as the accessibility of schools or the location of rescue service units. This platform will serve as a base for further large scale epidemiological and transportation simulation studies. However, the first approach to a simple, country-wide transportation model is also presented here. The application scope of the platform extends beyond the simulations of epidemic or transportation, and pertains to any situation where there are no easily available means, other than computer simulations, to conduct large scale investigations of complex population dynamics.Agent Based Model, Educational Availability, Daily Commuting, Social Network, Virtual Society Simulations

National and subnational short-term forecasting of COVID-19 in Germany and Poland during early 2021

We compare forecasts of weekly case and death numbers for COVID-19 in Germany and Poland based on 15 different modelling approaches. These cover the period from January to April 2021 and address numbers of cases and deaths one and two weeks into the future, along with the respective uncertainties. We find that combining different forecasts into one forecast can enable better predictions. However, case numbers over longer periods were challenging to predict. Additional data sources, such as information about different versions of the SARS-CoV-2 virus present in the population, might improve forecasts in the future

Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost.

The detailed knowledge of C. elegans connectome for 3 decades has not contributed dramatically to our understanding of worm's behavior. One of main reasons for this situation has been the lack of data on the type of synaptic signaling between particular neurons in the worm's connectome. The aim of this study was to determine synaptic polarities for each connection in a small pre-motor circuit controlling locomotion. Even in this compact network of just 7 neurons the space of all possible patterns of connection types (excitation vs. inhibition) is huge. To deal effectively with this combinatorial problem we devised a novel and relatively fast technique based on genetic algorithms and large-scale parallel computations, which we combined with detailed neurophysiological modeling of interneuron dynamics and compared the theory to the available behavioral data. As a result of these massive computations, we found that the optimal connectivity pattern that matches the best locomotory data is the one in which all interneuron connections are inhibitory, even those terminating on motor neurons. This finding is consistent with recent experimental data on cholinergic signaling in C. elegans, and it suggests that the system controlling locomotion is designed to save metabolic energy. Moreover, this result provides a solid basis for a more realistic modeling of neural control in these worms, and our novel powerful computational technique can in principle be applied (possibly with some modifications) to other small-scale functional circuits in C. elegans

Synaptic polarity of the command interneurons for Caenorhabditis Elegans directional motion

The command interneuron circuit for Caenorhabditis Elegans locomotion has been known for a long time [1,2]. However, synaptic polarities of these interneurons, and thus, the circuit functioning is largely unknown. Additionally, nematode command neurons express both glutamate-gated chloride channels and glutamate-gated cation channels, which causes that each synapse, even when belonging to the same neuron, might be either inhibitory or excitatory. We use an experimental behavioral data set: eighteen different neural ablations were performed and times spent in the forward and reverse motions were registered. Therefore one can consider eighteen different command neuron network structures where each one as a whole, controls the behavior of the nematode, and results with one of the eighteen different behavioral patterns. In order to decipher the particular polarities of each neuron we have constructed a theoretical (inter)neuron network model, in which neural activities are represented by a set of differential equations and searched all possible synaptic polarity combinations in the circuit to find the best match to the timing data [3,4]. Here, we present the extension of this model, where we explicitly incorporate calcium concentration dynamics as the regulatory factor and detailed connectivity diagram based on the transmission type of each synapse. Since the parameter space spanned by the morphological and regulatory factors is huge, we have applied an evolutionary strategy for finding the parameters of the mathematical model, for which the theoretical results and the experimental data fit the best. The overall model output consists of the averaged values: neuron activities, calcium concentration levels, input signal (the upstream neurons activity pattern) and of the resolved detailed connectivity diagram. The deciphered list of the types of synapses states that most of the synapses, including strongest connections, e.g. ASH -> “backward” motoneurons, PVC -> “forward” motoneurons, AVD -> AVA, in the command neuron circuit are inhibitory. <br/

SED as a function of input strength.

<p>All other circuit parameters are kept fixed as optimal.</p

Stationary calcium concentration of each interneuron depends on ablation type.

<p>This is analogous to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005834#pcbi.1005834.g009" target="_blank">Fig 9</a>.</p

Effect of single synaptic polarity switch on SED.

<p>Switching the polarity of a single connection above a baseline with all inhibitory connections can have diverse impact on SED, from vary weak to very strong. The switched connections are labeled in the top and their corresponding strengths are shown in the bottom. The first point on the right corresponds to the configuration with all excitatory synapses. For all points, the inputs to the interneurons are fixed and optimal.</p

Optimal input pattern to pre-motor interneurons (<i>σ</i>_<i>i</i>) for “mean weights” case.

<p>Optimal input pattern to pre-motor interneurons (<i>σ</i>_<i>i</i>) for “mean weights” case.</p

SED as a function of calcium related ionic conductances.

<p>Similar as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005834#pcbi.1005834.g008" target="_blank">Fig 8</a>. (A) Global view and (B) more local view.</p