LIVIVO - Search results -

Search results

Result 1 - 10 of total 29

Search options

Article ; Online: Modular Control of Biological Networks.

Murrugarra, David / Veliz-Cuba, Alan / Dimitrova, Elena / Kadelka, Claus / Wheeler, Matthew / Laubenbacher, Reinhard

ArXiv

2024

Abstract: The concept of control is central to understanding and applications of biological network models. Some of their key structural features relate to control functions, through gene regulation, signaling, or metabolic mechanisms, and computational models ... ...

Abstract	The concept of control is central to understanding and applications of biological network models. Some of their key structural features relate to control functions, through gene regulation, signaling, or metabolic mechanisms, and computational models need to encode these. Applications of models often focus on model-based control, such as in biomedicine or metabolic engineering. This paper presents an approach to model-based control that exploits two common features of biological networks, namely their modular structure and canalizing features of their regulatory mechanisms. The paper focuses on intracellular regulatory networks, represented by Boolean network models. A main result of this paper is that control strategies can be identified by focusing on one module at a time. This paper also presents a criterion based on canalizing features of the regulatory rules to identify modules that do not contribute to network control and can be excluded. For even moderately sized networks, finding global control inputs is computationally very challenging. The modular approach presented here leads to a highly efficient approach to solving this problem. This approach is applied to a published Boolean network model of blood cancer large granular lymphocyte (T-LGL) leukemia to identify a minimal control set that achieves a desired control objective.
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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

Dimitrova, Elena S / Knapp, Adam C / Stigler, Brandilyn / Stillman, Michael E

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 11

Abstract: 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 ... ...

Abstract	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.com/discretedynamics/cyclone under the Apache-2.0 license.
MeSH term(s)	Cyclonic Storms ; Computer Simulation ; Software
Language	English
Publishing date	2023-10-18
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad634
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2374: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

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

Trendafilova, Elina / Dimitrova, Elena / Didon, Jean-Philippe / Krasteva, Vessela

Diagnostics (Basel, Switzerland)

2021 Volume 11, Issue 6

Abstract: 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 ... ...

Abstract	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. Eligible patients admitted for elective CVS of atrial fibrillation (AF) between February 2019 and March 2020 were alternately randomized to treatment with either a PB defibrillator (DEFIGARD TOUCH7, Schiller Médical, Wissembourg, France) or a BTE high-energy (BTE-HE) defibrillator (LIFEPAK15, Physio-Control Inc., Redmond, WA, USA). Fixed-energy protocol (200-200-200 J) was administered. CVS success was accepted if sinus rhythm was restored at 1 min post-shock. The study design considered non-inferiority testing of the primary outcome: cumulative delivered energy (CDE). Seventy-three out of 78 randomized patients received allocated intervention: 38 BTE-HE (52%), 35 PB (48%). Baseline characteristics were well-balanced between groups (
Language	English
Publishing date	2021-06-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics11061107
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Book ; Online: A unified approach to reverse engineering and data selection for unique network identification

Veliz-Cuba, Alan / Newsome-Slade, Vanessa / Dimitrova, Elena S.

2022

Abstract: Due to cost concerns, it is optimal to gain insight into the connectivity of biological and other networks using as few experiments as possible. Data selection for unique network connectivity identification has been an open problem since the introduction ...

Abstract	Due to cost concerns, it is optimal to gain insight into the connectivity of biological and other networks using as few experiments as possible. Data selection for unique network connectivity identification has been an open problem since the introduction of algebraic methods for reverse engineering for almost two decades. In this manuscript we determine what data sets uniquely identify the unsigned wiring diagram corresponding to a system that is discrete in time and space. Furthermore, we answer the question of uniqueness for signed wiring diagrams for Boolean networks. Computationally, unsigned and signed wiring diagrams have been studied separately, and in this manuscript we also show that there exists an ideal capable of encoding both unsigned and signed information. This provides a unified approach to studying reverse engineering that also gives significant computational benefits. Comment: 21 pages
Keywords	Mathematics - Algebraic Geometry ; Mathematics - Dynamical Systems ; Quantitative Biology - Quantitative Methods
Subject code	000
Publishing date	2022-12-10
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Book ; Online: Quantifying the Total Effect of Edge Interventions in Discrete Multistate Networks

Murrugarra, David / Dimitrova, Elena

2019

Abstract: Developing efficient computational methods to assess the impact of external interventions on the dynamics of a network model is an important problem in systems biology. This paper focuses on quantifying the global changes that result from the application ...

Abstract	Developing efficient computational methods to assess the impact of external interventions on the dynamics of a network model is an important problem in systems biology. This paper focuses on quantifying the global changes that result from the application of an intervention to produce a desired effect, which we define as the total effect of the intervention. The type of mathematical models that we will consider are discrete dynamical systems which include the widely used Boolean networks and their generalizations. The potential interventions can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. We use a class of regulatory rules called nested canalizing functions that frequently appear in published models and were inspired by the concept of canalization in evolutionary biology. In this paper, we provide a polynomial normal form based on the canalizing properties of regulatory functions. Using this polynomial normal form, we give a set of formulas for counting the maximum number of transitions that will change in the state space upon an edge deletion in the wiring diagram. These formulas rely on the canalizing structure of the target function since the number of changed transitions depends on the canalizing layer that includes the input to be deleted. We also present computations on random networks to compare the exact number of changes with the upper bounds provided by our formulas. Finally, we provide statistics on the sharpness of these upper bounds in random networks. Comment: 10 pages, 8 figures
Keywords	Quantitative Biology - Molecular Networks
Subject code	000
Publishing date	2019-06-22
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Book ; Online: Revealing the canalizing structure of Boolean functions

Dimitrova, Elena / Stigler, Brandilyn / Kadelka, Claus / Murrugarra, David

Algorithms and applications

2021

Abstract: Boolean functions can be represented in many ways including logical forms, truth tables, and polynomials. Additionally, Boolean functions have different canonical representations such as minimal disjunctive normal forms. Other canonical representation is ...

Abstract	Boolean functions can be represented in many ways including logical forms, truth tables, and polynomials. Additionally, Boolean functions have different canonical representations such as minimal disjunctive normal forms. Other canonical representation is based on the polynomial representation of Boolean functions where they can be written as a nested product of canalizing layers and a polynomial that contains the noncanalizing variables. In this paper we study the problem of identifying the canalizing layers format of Boolean functions. First, we show that the problem of finding the canalizing layers is NP-hard. Second, we present several algorithms for finding the canalizing layers of a Boolean function, discuss their complexities, and compare their performances. Third, we show applications where the computation of canalizing layers can be used for finding a disjunctive normal form of a nested canalizing function. Another application deals with the reverse engineering of Boolean networks with a prescribed layering format. Finally, implementations of our algorithms in Python and in the computer algebra system Macaulay2 are available at https://github.com/ckadelka/BooleanCanalization. Comment: 17 pages, 2 figures
Keywords	Computer Science - Computational Complexity ; Quantitative Biology - Quantitative Methods
Subject code	511
Publishing date	2021-06-11
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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

Lavignasse, Delphine / Trendafilova, Elina / Dimitrova, Elena / Krasteva, Vessela

Journal of atrial fibrillation

2019 Volume 12, Issue 3, Page(s) 2172

Abstract: 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 ...

Abstract	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). The protocol was stopped at successful cardioversion (sinus rhythm at 1 minute post-shock), otherwise after the 3rd shock. If the 3rd BTE shock failed, a monophasic shock of 360J was delivered. Results: From May 2008 to November 2017, 193 patients (153 PE, 40 LE) were included in the study. Both groups significantly differed in a few characteristics, including chest circumference (p<0.05). After adjustment, the success rate was not significantly different for the two waveforms (94.5% PE vs 92.5% LE, Odds Ratio [95% Confidence Interval] = 0.25 [0.03-2.2]).There was no difference in safety: post-shock changes in Hsc-TnI levels were similar (p=0.25). The efficient cumulative energy was particularly related with BSA (β = 131.5, p=0.05), AF/AFL duration (β = 0.24, p=0.01) and gender (β = 61.8, p=0.05). Conclusions: The major clinical implications of this study concern the high success rate of cardioversion with both biphasic pulses and no superiority of LE over PE waveform with an excellent safety profile without post-shock myocardial injuries.
Language	English
Publishing date	2019-10-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2451936-4
ISSN	1941-6911
ISSN	1941-6911
DOI	10.4022/jafib.2172
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Molecular network control through boolean canalization.

Murrugarra, David / Dimitrova, Elena S

EURASIP journal on bioinformatics & systems biology

2015 Volume 2015, Issue 1, Page(s) 9

Abstract: 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 ... ...

Abstract	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. This work studies the role of canalization in the control of Boolean molecular networks. It provides a method for identifying the potential edges to control in the wiring diagram of a network for avoiding undesirable state transitions. The method is based on identifying appropriate input-output combinations on undesirable transitions that can be modified using the edges in the wiring diagram of the network. Moreover, a method for estimating the number of changed transitions in the state space of the system as a result of an edge deletion in the wiring diagram is presented. The control methods of this paper were applied to a mutated cell-cycle model and to a
Language	English
Publishing date	2015-11-04
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2233385-X
ISSN	1687-4153 ; 1687-4145
ISSN (online)	1687-4153
ISSN	1687-4145
DOI	10.1186/s13637-015-0029-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Book ; Online: Algebraic Experimental Design

Dimitrova, Elena S. / Fredrickson, Cameron H. / Rondoni, Nicholas A. / Stigler, Brandilyn / Veliz-Cuba, Alan

Theory and Computation

2022

Abstract: Over the past several decades, algebraic geometry has provided innovative approaches to biological experimental design that resolved theoretical questions and improved computational efficiency. However, guaranteeing uniqueness and perfect recovery of ... ...

Abstract	Over the past several decades, algebraic geometry has provided innovative approaches to biological experimental design that resolved theoretical questions and improved computational efficiency. However, guaranteeing uniqueness and perfect recovery of models are still open problems. In this work we study the problem of uniqueness of wiring diagrams. We use as a modeling framework polynomial dynamical systems and utilize the correspondence between simplicial complexes and square-free monomial ideals from Stanley-Reisner theory to develop theory and construct an algorithm for identifying input data sets $V\subset \mathbb F_p^n$ that are guaranteed to correspond to a unique minimal wiring diagram regardless of the experimental output. We apply the results on a tumor-suppression network mediated by epidermal derived growth factor receptor and demonstrate how careful experimental design decisions can lead to a unique minimal wiring diagram identification. One of the insights of the theoretical work is the connection between the uniqueness of a wiring diagram for a given $V\subset \mathbb F_p^n$ and the uniqueness of the reduced Gr\"obner basis of the polynomial ideal $I(V)\subset \mathbb F_p[x_1,\ldots, x_n]$. We discuss existing results and introduce a new necessary condition on the points in $V$ for uniqueness of the reduced Gr\"obner basis of $I(V)$. These results also point to the importance of the relative proximity of the experimental input points on the number of minimal wiring diagrams, which we then study computationally. We find that there is a concrete heuristic way to generate data that tends to result in fewer minimal wiring diagrams. Comment: 16 pages, 2 figures (one in color but prints well in b&w), 2 tables
Keywords	Mathematics - Algebraic Geometry ; Quantitative Biology - Molecular Networks ; 11T06 ; 92C42 ; 37N25 ; 13F55
Subject code	000 ; 004
Publishing date	2022-08-04
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Geometric Characterization of Data Sets with Unique Reduced Gröbner Bases.

He, Qijun / Dimitrova, Elena S / Stigler, Brandilyn / Zhang, Anyu

Bulletin of mathematical biology

2019 Volume 81, Issue 7, Page(s) 2691–2705

Abstract: 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 ... ...

Abstract	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. We use linear shifts to partition data into equivalence classes with the same basis. We demonstrate the utility of the results by applying them to a Boolean model of the well-studied lac operon in E. coli.
MeSH term(s)	Algorithms ; Databases, Factual ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Lac Operon ; Linear Models ; Mathematical Concepts ; Models, Biological ; Systems Biology
Language	English
Publishing date	2019-06-29
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	184905-0
ISSN	1522-9602 ; 0007-4985 ; 0092-8240
ISSN (online)	1522-9602
ISSN	0007-4985 ; 0092-8240
DOI	10.1007/s11538-019-00624-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.B 754: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito