scholarly journals An analytical approach to bistable biological circuit discrimination using real algebraic geometry

2014 ◽  
Author(s):  
Dan Siegal-Gaskins ◽  
Elisa Franco ◽  
Tiffany Zhou ◽  
Richard M Murray
Keyword(s):  
Algebraic Geometry ◽  
Circuit Design ◽  
Biological Networks ◽  
Predictive Power ◽  
Real Algebraic Geometry ◽  
Ease Of Use ◽  
Topological Properties ◽  
Essential Components ◽  
Wide Range ◽  
Geometric Techniques

Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm?s theorem--a tool from 19th-century real algebraic geometry--to comparing ?functionally equivalent? bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely-monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh-Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm?s theorem demonstrated in this work suggests that algebraic geometric techniques may be underutilized in biomolecular circuit analysis.

scholarly journals An analytical approach to bistable biological circuit discrimination using real algebraic geometry

2015 ◽  
Vol 12 (108) ◽  
pp. 20150288 ◽  
Author(s):  
Dan Siegal-Gaskins ◽  
Elisa Franco ◽  
Tiffany Zhou ◽  
Richard M. Murray
Keyword(s):  
Algebraic Geometry ◽  
Circuit Design ◽  
Biological Networks ◽  
Predictive Power ◽  
Real Algebraic Geometry ◽  
Ease Of Use ◽  
Topological Properties ◽  
Essential Components ◽  
Wide Range ◽  
Geometric Techniques

Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm's theorem—a tool from nineteenth-century real algebraic geometry—to comparing ‘functionally equivalent’ bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh–Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm's theorem demonstrated in this work suggest that algebraic geometric techniques may be underused in biomolecular circuit analysis.

From the history of the development of electronic dictionaries: foreign and domestic experience

2020 ◽  
Vol 11 (1) ◽  
pp. 6-12
Author(s):  
O. Y. Balalaieva ◽  
Keyword(s):  
Human Activity ◽  
Current Level ◽  
Ease Of Use ◽  
Advanced Search ◽  
Wide Range ◽  
Promising Area ◽  
History Of ◽  
Machine Readable ◽  
Everyday Communication ◽  
Educational Professional

The purpose of the article is to study the dynamics of electronic dictionaries development abroad and in Ukraine using methods of analysis of scientific sources, comparison, generalization and systematization. Electronic dictionaries have been found to be a relatively new phenomenon in the lexicographic market, evolving from machine-readable dictionaries, exact copies of paper editions to complex digital lexicographic systems with a powerful arsenal of functions over the decades. The stages of development of autonomous and online dictionaries are described. Electronic dictionaries due to the advanced search capabilities, speed, simplicity, ease of use, accessibility and compactness have gained popularity among a wide range of users. Today they are used in many spheres of human activity – scientific, educational, professional, everyday communication. However, the analysis of the current level of development of Ukrainian electronic resources indicates a shortage of electronic dictionaries both common and terminological vocabulary. The lack of electronic dictionaries is due to a number of objective problems, both practical and theoretical, that is why research in the field of domestic computer lexicography is a promising area of further research.

Nanoparticles Functionalized with Venom-Derived Peptides and Toxins for Pharmaceutical Applications

2020 ◽  
Vol 21 (2) ◽  
pp. 97-109 ◽  
Author(s):  
Ana P. dos Santos ◽  
Tamara G. de Araújo ◽  
Gandhi Rádis-Baptista
Keyword(s):  
Oral Absorption ◽  
Current Data ◽  
Pharmacological Activities ◽  
Venom Peptides ◽  
Essential Components ◽  
Wide Range ◽  
Different Types ◽  
Direct Use ◽  
Animal Venoms ◽  
Pharmaceutical Biotechnology

Venom-derived peptides display diverse biological and pharmacological activities, making them useful in drug discovery platforms and for a wide range of applications in medicine and pharmaceutical biotechnology. Due to their target specificities, venom peptides have the potential to be developed into biopharmaceuticals to treat various health conditions such as diabetes mellitus, hypertension, and chronic pain. Despite the high potential for drug development, several limitations preclude the direct use of peptides as therapeutics and hamper the process of converting venom peptides into pharmaceuticals. These limitations include, for instance, chemical instability, poor oral absorption, short halflife, and off-target cytotoxicity. One strategy to overcome these disadvantages relies on the formulation of bioactive peptides with nanocarriers. A range of biocompatible materials are now available that can serve as nanocarriers and can improve the bioavailability of therapeutic and venom-derived peptides for clinical and diagnostic application. Examples of isolated venom peptides and crude animal venoms that have been encapsulated and formulated with different types of nanomaterials with promising results are increasingly reported. Based on the current data, a wealth of information can be collected regarding the utilization of nanocarriers to encapsulate venom peptides and render them bioavailable for pharmaceutical use. Overall, nanomaterials arise as essential components in the preparation of biopharmaceuticals that are based on biological and pharmacological active venom-derived peptides.

Designing Soft Reactive Adhesives by Controlling Polymer Chemistry

MRS Bulletin ◽  
2003 ◽  
Vol 28 (6) ◽  
pp. 424-427 ◽  
Author(s):  
Agnès Aymonier ◽  
Eric Papon
Keyword(s):  
Automotive Industry ◽  
Ease Of Use ◽  
Large Strains ◽  
Structural Adhesives ◽  
Wide Range ◽  
Step Growth ◽  
Visible Irradiation ◽  
Step Growth Polymerization ◽  
Uv Visible ◽  
Activation Heat

AbstractSoft reactive adhesives (SRAs) are polymer-based materials (e.g., polyurethanes, polysiloxanes, polydienes) designed to be further vulcanized or slightly cross-linked through external activation (heat, moisture, oxygen, UV–visible irradiation, etc.), either at the time of their application or within a subsequent predefined period. They are used mainly as mastics, or sealing compounds, in a wide range of industrial and commercial fields such as construction, footwear, and the automotive industry. Generally deposited as thick films, SRAs behave as structural adhesives; their low elastic moduli accommodate large strains between the bonded parts without incurring permanent damage. Other outstanding attributes of SRAs are their resistance to solvents, their ability to withstand aggressive environments, and their ease of use. This article discusses examples of SRAs and, more specifically, shows how the cross-linking chemistry, mainly through step-growth polymerization, provides their primary advantages.

scholarly journals TOPOLOGICAL CELL DECOMPOSITION AND DIMENSION THEORY IN P-MINIMAL FIELDS

2017 ◽  
Vol 82 (1) ◽  
pp. 347-358 ◽  
Author(s):  
PABLO CUBIDES KOVACSICS ◽  
LUCK DARNIÈRE ◽  
EVA LEENKNEGT
Keyword(s):  
Algebraic Geometry ◽  
Open Subset ◽  
Cell Decomposition ◽  
Real Algebraic Geometry ◽  
Dimension Theory ◽  
Definable Set ◽  
Image Position ◽  
Definable Function

AbstractThis paper addresses some questions about dimension theory for P-minimal structures. We show that, for any definable set A, the dimension of $\bar A\backslash A$ is strictly smaller than the dimension of A itself, and that A has a decomposition into definable, pure-dimensional components. This is then used to show that the intersection of finitely many definable dense subsets of A is still dense in A. As an application, we obtain that any definable function $f:D \subseteq {K^m} \to {K^n}$ is continuous on a dense, relatively open subset of its domain D, thereby answering a question that was originally posed by Haskell and Macpherson.In order to obtain these results, we show that P-minimal structures admit a type of cell decomposition, using a topological notion of cells inspired by real algebraic geometry.

Ultrasonographic Applications in the Thorax

2021 ◽  
Vol 18 ◽  
Author(s):  
Mehmet Zeki Gunluoglu ◽  
Tugrul Ormeci ◽  
Selva Sen
Keyword(s):  
Emergency Department ◽  
Intensive Care ◽  
Pleural Effusion ◽  
Respiratory System ◽  
Ease Of Use ◽  
Endobronchial Ultrasound ◽  
Access Price ◽  
Wide Range ◽  
Diagnostic Sensitivity And Specificity ◽  
Fast Access

Abstract: Rapid developments and increasing technological knowledge have changed perspectives on ultrasonography. Previously, ultrasonography was used to evaluate chest wall pathologies, to distinguish between pleural effusion and consolidation, to evacuate pleural effusion, or to evaluate diaphragm movement. Today, it is also used in a wide range of pleural and parenchymal diseases. Ultrasonography is not just used in the emergency department and the intensive care units. It is also utilized in many clinical branches dealing with the respiratory system—due to its ease of use, fast access, price advantage, non-radiation exposure, higher diagnostic sensitivity, and specificity in many clinical situations—and has become a part of the examination. In this review, we have assessed not just transthoracic ultrasonography but also more focal and targeted sonographic applications, such as the endobronchial ultrasound and esophageal ultrasound.

Detection of Random Responding in MMPI-2 Protocols

Assessment ◽  
1996 ◽  
Vol 3 (2) ◽  
pp. 171-178 ◽  
Author(s):  
Robert T. Gallen ◽  
David T. R. Berry
Keyword(s):  
Predictive Power ◽  
Minnesota Multiphasic Personality Inventory ◽  
Present Report ◽  
Ease Of Use ◽  
Variable Response ◽  
Random Responding ◽  
Base Rates ◽  
Validity Indices ◽  
Alternative Index ◽  
Hit Rates

The present report represents a replication and extension of the Berry et al. (1991) study examining the utility of the standard second edition of the Minnesota Multiphasic Personality Inventory (MMPI-2) validity indices for detecting random responding. Specifically, relative to Berry et al., this study employs methodological improvements and investigates recently proposed alternative indices for detecting random responding. Another improvement includes the use of Bayesian statistics, including positive predictive power, negative predictive power, and hit rates, to select various cutting scores across three base rates of random responding. Results suggested that all validity indices studied differed significantly between random and valid protocols, although certain indices provided for more optimal hit rates in terms of classification. It is concluded that the alternative index, Variable Response Inconsistency ( VRIN) scale plus the Infrequency ( F) scale minus the Infrequency Back ( FB) scale ( VRIN + | F - FB|) provided for the highest hit rate across all examined base rates of random responding. However, VRIN also provided for highly accurate classification rates and has specific advantages including the scale's repeated validation in the literature, its ease of use, and empirical findings suggesting that the scale is insensitive to overreporting.

scholarly journals A Representation Theorem for Archimedean Quadratic Modules on ∗-Rings

2009 ◽  
Vol 52 (1) ◽  
pp. 39-52 ◽  
Author(s):  
Jakob Cimprič
Keyword(s):  
Algebraic Geometry ◽  
Representation Theory ◽  
Representation Theorem ◽  
Commutative Rings ◽  
Real Algebraic Geometry ◽  
New Approach ◽  
Noncommutative Version ◽  
Quadratic Modules ◽  
Rings With Involution ◽  
Associative Rings

AbstractWe present a new approach to noncommutative real algebraic geometry based on the representation theory of C*-algebras. An important result in commutative real algebraic geometry is Jacobi's representation theorem for archimedean quadratic modules on commutative rings. We show that this theorem is a consequence of the Gelfand–Naimark representation theorem for commutative C*-algebras. A noncommutative version of Gelfand–Naimark theory was studied by I. Fujimoto. We use his results to generalize Jacobi's theorem to associative rings with involution.

scholarly journals pyTFM: A tool for traction force and monolayer stress microscopy

2021 ◽  
Vol 17 (6) ◽  
pp. e1008364
Author(s):  
Andreas Bauer ◽  
Magdalena Prechová ◽  
Lena Fischer ◽  
Ingo Thievessen ◽  
Martin Gregor ◽  
...  
Keyword(s):  
Image Annotation ◽  
Traction Force ◽  
Theoretical Background ◽  
Ease Of Use ◽  
Traction Force Microscopy ◽  
Force Transmission ◽  
Force Microscopy ◽  
Wide Range ◽  
Cell Layers ◽  
Cellular Stresses

Cellular force generation and force transmission are of fundamental importance for numerous biological processes and can be studied with the methods of Traction Force Microscopy (TFM) and Monolayer Stress Microscopy. Traction Force Microscopy and Monolayer Stress Microscopy solve the inverse problem of reconstructing cell-matrix tractions and inter- and intra-cellular stresses from the measured cell force-induced deformations of an adhesive substrate with known elasticity. Although several laboratories have developed software for Traction Force Microscopy and Monolayer Stress Microscopy computations, there is currently no software package available that allows non-expert users to perform a full evaluation of such experiments. Here we present pyTFM, a tool to perform Traction Force Microscopy and Monolayer Stress Microscopy on cell patches and cell layers grown in a 2-dimensional environment. pyTFM was optimized for ease-of-use; it is open-source and well documented (hosted at https://pytfm.readthedocs.io/) including usage examples and explanations of the theoretical background. pyTFM can be used as a standalone Python package or as an add-on to the image annotation tool ClickPoints. In combination with the ClickPoints environment, pyTFM allows the user to set all necessary analysis parameters, select regions of interest, examine the input data and intermediary results, and calculate a wide range of parameters describing forces, stresses, and their distribution. In this work, we also thoroughly analyze the accuracy and performance of the Traction Force Microscopy and Monolayer Stress Microscopy algorithms of pyTFM using synthetic and experimental data from epithelial cell patches.

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