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Cytotoxic T lymphocytes eliminate infected or malignant cells, safeguarding surrounding tissues. Although experimental and systems-immunology studies have cataloged many molecular and cellular actors involved in an immune response, the…
"Concurrence topology" (Ellis and Klein \emph{Homology, Homotopy, and Applications,} \textbf{16}) is a TDA method for binary data. The idea is to construct a filtration consisting of Dowker complexes then compute persistent homology.…
We propose an extension of a standard stochastic individual-based model in population dynamics which broadens the range of biological applications. Our primary motivation is modelling of immunotherapy of malignant tumours. In this context…
Background: Mycobacterium Tuberculosis (TB) is an infectious bacterial disease presenting similar symptoms to pneumonia; therefore, differentiating between TB and pneumonia is challenging. Therefore, the main aim of this study is proposing…
This study here suggests a classification of technologies based on taxonomic characteristics of interaction between technologies in complex systems that is not a studied research field in economics of technical change. The proposed taxonomy…
The problem of \emph{statistical recognition} is considered, as it arises in immunobiology, namely, the discrimination of foreign antigens against a background of the body's own molecules. The precise mechanism of this…
The human adaptive immune response is known to weaken in advanced age, resulting in increased severity of pathogen-born illness, poor vaccine efficacy, and a higher prevalence of cancer in the elderly. Age-related erosion of the T-cell…
The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called $\alpha$ and $\beta$, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human…
Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the…
Reaction-diffusion systems may lead to the formation of steady state heterogeneous spatial patterns, known as Turing patterns. Their mathematical formulation is important for the study of pattern formation in general and play central roles…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…
We study the robustness of an evolving system that is driven by successive inclusions of new elements or constituents with $m$ random interactions to older ones. Each constitutive element in the model stays either active or is temporarily…
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…
T-cells are a crucial subset of white blood cells that play a central role in the immune system. When T-cells bind antigens, it leads to cell activation and the induction of an immune response. If T-cells are activated by antigens in vivo…
The density matrix of a two-level system (spin, atom) is usually determined by measuring the three non-commuting components of the Pauli vector. This density matrix can also be obtained via the measurement data of two commuting variables,…
We study a system in which N agents have to decide between two strategies \theta_i (i \in 1... N), for defection or cooperation, when interacting with other n agents (either spatial neighbors or randomly chosen ones). After each round, they…
We present a mechanism for detecting adversarial examples based on data representations taken from the hidden layers of the target network. For this purpose, we train individual autoencoders at intermediate layers of the target network.…
The classification of bunching of straight steps on vicinal crystal surfaces identifies two types according to the behavior of the minimal step-step distance in the bunch lmin with increasing the number of steps N in it. In the B1-type lmin…
Cells can sense forces applied to them, but also the stiffness of their environment. These are two different phenomena, and here we investigate the mechanosensitivity of the IInd kind: how the cell can measure an elastic modulus at a single…
Confirming Turing's theory of morphogens in developmental processes is challenging, and synthetic biology has opened new avenues for testing Turing's predictions. Synthetic mammalian pattern formation has been recently achieved through a…