Modular control of Boolean network models.

The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational models need to encode these. Applications often focus on model-based control, such as in biomedicine or metabolic engineering.

Cyclone: open-source package for simulation and analysis of finite dynamical systems.

Motivation: While there are software packages that analyze Boolean, ternary, or other multi-state models, none compute the complete state space of function-based models over any finite set. Results: We propose Cyclone, a simple light-weight software package which simulates the complete state space for a finite dynamical system over any finite set.

Availability And Implementation: Source code is freely available at https://github.

A Randomized Comparison of Delivered Energy in Cardioversion of Atrial Fibrillation: Biphasic Truncated Exponential Versus Pulsed Biphasic Waveforms.

A few randomized trials have compared impedance-compensated biphasic defibrillators in clinical use. We aim to compare pulsed biphasic (PB) and biphasic truncated exponential (BTE) waveforms in a non-inferiority cardioversion (CVS) study. This was a prospective monocentric randomized clinical trial.

Cardioversion of Atrial Fibrillation and Flutter: Comparative Study of Pulsed vs. Low Energy Biphasic Truncated Exponential Waveforms.

Background: Despite the widespread use of biphasic waveforms for cardioversion and defibrillation, the efficacy and safety of shocks has only been compared in a few studies.

Methods: This retrospective study aims at comparing the efficacy and safety of biphasic truncated exponential (BTE) pulsed energy (PE) waveform with a BTE low energy (LE) waveform for cardioversion of atrial fibrillation (AF) and atrial flutter (AFL). The treatment energies were following an escalating protocol for PE waveform (120-200-200J in AF and 30-120-200J in AFL) and LE waveform (100-200-200J in AF and 30-100-200J in AFL).

Geometric Characterization of Data Sets with Unique Reduced Gröbner Bases.

Model selection based on experimental data is an important challenge in biological data science. Particularly when collecting data is expensive or time-consuming, as it is often the case with clinical trial and biomolecular experiments, the problem of selecting information-rich data becomes crucial for creating relevant models. We identify geometric properties of input data that result in an unique algebraic model, and we show that if the data form a staircase, or a so-called linear shift of a staircase, the ideal of the points has a unique reduced Gröbner basis and thus corresponds to a unique model.

The innate immune response to ischemic injury: a multiscale modeling perspective.

Background: Cell death as a result of ischemic injury triggers powerful mechanisms regulated by germline-encoded Pattern Recognition Receptors (PRRs) with shared specificity that recognize invading pathogens and endogenous ligands released from dying cells, and as such are essential to human health. Alternatively, dysregulation of these mechanisms contributes to extreme inflammation, deleterious tissue damage and impaired healing in various diseases. The Toll-like receptors (TLRs) are a prototypical family of PRRs that may be powerful anti-inflammatory targets if agents can be designed that antagonize their harmful effects while preserving host defense functions.

The Patterns of Non-vitamin K Antagonist Oral Anticoagulants (NOACs) Use in Patients with Atrial Fibrillation in Seven Balkan Countries: a Report from the BALKAN-AF Survey.

Introduction: Data on management of atrial fibrillation (AF) in the Balkan Region are scarce. To capture the patterns in AF management in contemporary clinical practice in the Balkan countries a prospective survey was conducted between December 2014 and February 2015, and we report results pertinent to the use of non-vitamin K antagonist oral anticoagulants (NOACs).

Methods: A 14-week prospective, multicenter survey of consecutive AF patients seen by cardiologists or internal medicine specialists was conducted in Albania, Bosnia and Herzegovina, Bulgaria, Croatia, Montenegro, Romania, and Serbia (a total of about 50 million inhabitants).

Stroke prevention in atrial fibrillation and 'real world' adherence to guidelines in the Balkan Region: The BALKAN-AF Survey.

Data on the management of atrial fibrillation (AF) in the Balkan Region are limited. The Serbian AF Association (SAFA) prospectively investigated contemporary 'real-world' AF management in clinical practice in Albania, Bosnia&Herzegovina, Bulgaria, Croatia, Montenegro, Romania and Serbia through a 14-week (December 2014-February 2015) prospective, multicentre survey of consecutive AF patients. We report the results pertinent to stroke prevention strategies.

Effects of carob-bean gum thickened formulas on infants' reflux and tolerance indices.

Aim: To examine the effect of carob-bean gum (CBG) thickened-formulas on reflux and tolerance indices in infants with gastro-esophageal reflux (GER).

Methods: Fifty-six eligible infants (1-6 mo old) were randomly allocated to receive for two weeks a formula with either 0.33 g/100 mL (Formula A) or 0.

Molecular network control through boolean canalization.

Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of network modeling where each layer of canalization adds a degree of stability in the dynamics of the network. Recently, dynamic network control approaches have been used for the design of new therapeutic interventions and for other applications such as stem cell reprogramming.

Difference equation for tracking perturbations in systems of Boolean nested canalyzing functions.

This paper studies the spread of perturbations through networks composed of Boolean functions with special canalyzing properties. Canalyzing functions have the property that at least for one value of one of the inputs the output is fixed, irrespective of the values of the other inputs. In this paper the focus is on partially nested canalyzing functions, in which multiple, but not all inputs have this property in a cascading fashion.

Data identification for improving gene network inference using computational algebra.

Identification of models of gene regulatory networks is sensitive to the amount of data used as input. Considering the substantial costs in conducting experiments, it is of value to have an estimate of the amount of data required to infer the network structure. To minimize wasted resources, it is also beneficial to know which data are necessary to identify the network.

Polynomial algebra reveals diverging roles of the unfolded protein response in endothelial cells during ischemia-reperfusion injury.

The unfolded protein response (UPR)--the endoplasmic reticulum stress response--is found in various pathologies including ischemia-reperfusion injury (IRI). However, its role during IRI is still unclear. Here, by combining two different bioinformatical methods--a method based on ordinary differential equations (Time Series Network Inference) and an algebraic method (probabilistic polynomial dynamical systems)--we identified the IRE1α-XBP1 and the ATF6 pathways as the main UPR effectors involved in cell's adaptation to IRI.

Nested canalyzing depth and network stability.

We introduce the nested canalyzing depth of a function, which measures the extent to which it retains a nested canalyzing structure. We characterize the structure of functions with a given depth and compute the expected activities and sensitivities of the variables. This analysis quantifies how canalyzation leads to higher stability in Boolean networks.

Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks.

Elucidating the structure and/or dynamics of gene regulatory networks from experimental data is a major goal of systems biology. Stochastic models have the potential to absorb noise, account for un-certainty, and help avoid data overfitting. Within the frame work of probabilistic polynomial dynamical systems, we present an algorithm for the reverse engineering of any gene regulatory network as a discrete, probabilistic polynomial dynamical system.

Discretization of time series data.

An increasing number of algorithms for biochemical network inference from experimental data require discrete data as input. For example, dynamic Bayesian network methods and methods that use the framework of finite dynamical systems, such as Boolean networks, all take discrete input. Experimental data, however, are typically continuous and represented by computer floating point numbers.