Background. The use of wavelet coherence methods enables the identification of frequency-dependent relationships between the phases of the fluctuations found in complex systems such as medical and other biological timeseries. These relationships may illuminate the causal mechanisms that relate the variables under investigation. However, computationally intensive statistical...
Background The Crigler-Najjar syndrome is extremely rare genetic disease, that is manifested by severe jaundicedue to lack of UDP glucuronosyltransferase 1-A1 (UDP) activity. The main treatment is to use the blue lightphototherapy, during the prolong time, during the day every day. Methods Here, we analyzed human UDP’s correlation with the blue light phototherapy using the...
Background Measuring the agreement between a gene expression profile and a known transcriptional regulatory network is an important step in the functional interpretation of bacterial physiological state. In this way, general design principles can be explored. One such interpretive framework is the relationship of digital control, that is, the impact of sequence-specific...
Background Measuring the agreement between a gene expression profile and a known transcriptional regulatory network is an important step in the functional interpretation of bacterial physiological state. In this way, general design principles can be explored. One such interpretive framework is the relationship of digital control, that is, the impact of sequence-specific...
Background Measuring the agreement between a gene expression profile and a known transcriptional regulatory network is an important step in the functional interpretation of bacterial physiological state. In this way, general design principles can be explored. One such interpretive framework is the relationship of digital control, that is, the impact of sequence-specific...
Systems Biology is a young and rapidly evolving research field, which combines experimental techniques and mathematical modeling in order to achieve a mechanistic understanding of processes underlying the regulation and evolution of living systems. Systems Biology is often associated with an Engineering approach: The purpose is to formulate a data-rich, detailed simulation model...
Background Noninvasive mechanical ventilation is sufficiently widely used to motivate bench studies for evaluating and comparing performances of the domiciliary ventilators. In most (if not in all) of the previous studies, ventilators were tested in a single (or a very few) conditions, chosen to avoid asynchrony events. Such a practice does not reflect how the ventilator is able...
Background Markov chain models of calcium release sites in living cells exhibit stochastic dynamics reminiscent of the experimentally observed phenomenon of calcium puffs and sparks. Such models often take the form of stochastic automata networks in which the transition probabilities for each of a large number of intercellular channel models depend on the local calcium...
BackgroundMathematical modeling of biological regulatory networks provides valuable insights into the structural and dynamical properties of the underlying systems. While dynamic models based on differential equations provide quantitative information on the biological systems, qualitative models that rely on the logical interactions among the components provide coarse-grained...
Background The description of intracellular processes based on chemical reaction kinetics has become a standard approach in the last decades, and parameter estimation poses several challenges. Sensitivity analysis is a powerful tool in model development that can aid model calibration in various ways. Results can for example be used to simplify the model by elimination or fixation...
Background The description of intracellular processes based on chemical reaction kinetics has become a standard approach in the last decades, and parameter estimation poses several challenges. Sensitivity analysis is a powerful tool in model development that can aid model calibration in various ways. Results can for example be used to simplify the model by elimination or fixation...
Background The recent experimental technique of chromosome conformational capture gives an in-vivo access to pairwise contact frequencies between genomic loci. We present how network analysis can be exploited to extract information from genome-wide contact maps. Methods We recently proposed to use graph distance for deriving a complete distance matrix from sparse contact maps...
Background The recent experimental technique of chromosome conformational capture gives an in-vivo access to pairwise contact frequencies between genomic loci. We present how network analysis can be exploited to extract information from genome-wide contact maps. Methods We recently proposed to use graph distance for deriving a complete distance matrix from sparse contact maps...
Background Pulmonary arterial hypertension is a rare and lethal disease affecting small diameter pulmonary arteries and leading to a progressive increase of the right vascular resistances. Patients with such a disease have no specific symptom, a feature which delays the diagnosis by 18 months to 2 years in average. In most cases, pulmonary arterial hypertension is diagnosed when...
Tomasetti and Vogelstein recently proposed that the majority of variation in cancer risk among tissues is due to “bad luck,” that is, random mutations arising during DNA replication in normal noncancerous stem cells. They generalize this finding to cancer overall, claiming that “the stochastic effects of DNA replication appear to be the major contributor to cancer in humans.” We...
Background A growing population is diagnosed with Attention Deficit Hyperactivity Disorder (ADHD) and are currently being treated with psychostimulants. Brain Computer Interface (BCI) is a method of communicating with an external program or device based on measured electrical signals from the brain. A particular brain signal, the P300 potential, can be measured about 300 ms after...
The absence of clear breakthrough in malaria combat could support the need for different ways of tackling the disease that are substantiated by conceptually new bases. The main idea of this research is to analyze possibility to interfere with malaria parasite activity using specific resonant electromagnetic frequencies. Although the idea to combat malaria infection with...
Tomasetti and Vogelstein recently proposed that the majority of variation in cancer risk among tissues is due to “bad luck,” that is, random mutations arising during DNA replication in normal noncancerous stem cells. They generalize this finding to cancer overall, claiming that “the stochastic effects of DNA replication appear to be the major contributor to cancer in humans.” We...
BackgroundBrain Computer Interface (BCI) is the method of transforming mental thoughts and imagination into actions. A real-time BCI system can improve the quality of life of patients with severe neuromuscular disorders by enabling them to communicate with the outside world. In this paper, the implementation of a 2-class real-time BCI system based on the event related...
Background The inverse relationship between movement speed and accuracy in goal-directed aiming is mostly investigated using the classic Fitts’ paradigm. According to Fitts’ law, movement time scales linearly with a single quantity, the index of difficulty (ID), which quantifies task difficulty through the quotient of target width and distance. Fitts’ law remains silent, however...
Genius is defined as a person of outstanding mental skills. These skills result from genius’ brain structure and physiology that are determined by genetics. It seems that environment and education may only inhibit development of a genius. Based on a simple model of brain phase space we formulate two hypotheses about dynamics of mental processes in genius’ brain and the difference...
Background In this report, we show how entropy computation can be applied to the characterization of a protein-protein interaction networks to assist the selection of personalized chemotherapeutic strategy for cancer treatment. Methods With seven malignant (BT-20, BT-474, MDA-MB-231, MDA-MB-468, MCF-7, T-47D, ZR-75-1) and one healthy (MCF10A) cell lines, we combined interactome...
Background It has been shown that there are electromagnetic resonances in biological molecules (proteins, DNA and RNA) in the wide range of frequencies including THz, GHz, MHz and KHz. These resonances could be important for biological function of macromolecules, as well as could be used in development of devices like molecular computers. As experimental measurements of...
Background It has been shown that there are electromagnetic resonances in biological molecules (proteins, DNA and RNA) in the wide range of frequencies including THz, GHz, MHz and KHz. These resonances could be important for biological function of macromolecules, as well as could be used in development of devices like molecular computers. As experimental measurements of...
Background The article is focused on the brain connectivity extensions and expansions, with the introductory elements in this section. Method In Causality measures and brain connectivity models, the necessary, basic properties demanded in the problem are summerized, which is followed by short introduction to Granger causality, Geweke developments, PDC, DTF measures, and short...
