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Diana David-Rus

Publications and source records attributed to Diana David-Rus.

5 recordsLinked to original sources

Inferring the effect of interventions on COVID-19 transmission networks

Countries around the world implement nonpharmaceutical interventions (NPIs) to mitigate the spread of COVID-19. Design of efficient NPIs requires identification of the structure of the disease transmission network. We here identify the key parameters of the COVID-19 transmission network for time periods before, during, and after the application of strict NPIs for the first wave of COVID-19 infections in Germany combining Bayesian parameter inference with an agent-based epidemiological model. We assume a Watts-Strogatz small-world network which allows to distinguish contacts within clustered cliques and unclustered, random contacts in the population, which have been shown to be crucial in sustaining the epidemic. In contrast to other works, which use coarse-grained network structures from anonymized data, like cell phone data, we consider the contacts of individual agents explicitly. We show that NPIs drastically reduced random contacts in the transmission network, increased network clustering, and resulted in a change from an exponential to a constant regime of newcases. In this regime, the disease spreads like a wave with a finite wave speed that depends on the number of contacts in a nonlinear fashion, which we can predict by mean field theory. Our analysis indicates that besides the well-known transitionbetween exponential increase and exponential decrease in the number of new cases, NPIs can induce a transition to another, previously unappreciated regime of constant new cases.

q-bio.PE

Protein Synthesis- Degradation, A Stochastic Approach-part I

In this work, we study a protein synthesis degradation process by defining a general mathematical model. Using generating function technique we present a method that allows exact calculation of joint probability distribution of protein copies in a cell for a two dimensional birth-death process with interaction. We discuss the model in steady state for a particular choice of transition rules and find exact solutions.

q-bio.QM

Quantitative transcriptional analysis of aging C. elegans

My analysis uses methods developed for data mining microarray experiments, adapted for ageing research. Methods bridge knowledge of statistical mechanics with data mining methods developed in statistical mathematics. Analyses can reveal how the transcriptional regulation of genes might coincide, thereby implicating proteins as parts of networks acting together towards a common biological function. Such experiments are most useful for complex biological traits that result from the presumed functioning of several molecular pathways. Ageing is one such biological phenomenon that apparently incorporates numerous molecular mechanisms underlying environmental stimulus sensing, metabolic regulation, stress responses, reproductive signalling, hibernation, and transcriptional regulation.

q-bio.QM

In the search of molecular signature of sarcopenia in C. elegans

Age-related muscle decline, a condition referred to as sarcopenia and defined as loss in muscle mass and muscle strength over time, is one of the most pervasive problems of the elderly, such that significant declines in strength and mobility affects essentially every old person We have found that ageing C. elegans body wall muscle undergoes a process remarkably reminiscent of human sarcopenia. Both have mid-life onset and are characterized by progressive loss of sarcomeres and cytoplasmic volume; both are associated with locomotory decline. To extend understanding of this fundamental problem, I surveyed expression of all known muscle related genes to describe a profile of transcriptional changes in muscle that transpires during adult life and ageing. Importantly, the intersection of this dataset with that from ageing flies and some human studies can suggest conserved genes that might impact the process most strongly. Hypotheses I formulate will be used to drive experiments at the bench and perhaps to focus attention for human therapies.

q-bio.QM

Mathematical framework of epigenetic DNA methylation in gene body Arabidopsis

In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues are maintained and transmitted during DNA replication. Routed in statistical mechanics, the framework built herein is used to explore minimal models of epigenetic inheritance and identify the necessary conditions for stability of methylated/unmethylated states of cytosine over rounds of DNA replication. The models are flexible enough to allow adding new biological concepts and information.

q-bio.QM