Model-based design of synthetic, biological systems

2013 ◽  
Vol 103 ◽  
pp. 2-11 ◽  
Author(s):  
Nathan Crook ◽  
Hal S. Alper
Keyword(s):  
Biological Systems ◽  
Model Based

Model-based and data-driven with multiscale sum of squares double EWMA control chart for fault detection in biological systems

2018 ◽  
Vol 32 (12) ◽  
pp. e3068 ◽  
Author(s):  
Majdi Mansouri ◽  
Mohamed Faouzi Harkat ◽  
Sin Yin Teh ◽  
Ayman Al-khazraji ◽  
Hazem Nounou ◽  
...  
Keyword(s):  
Fault Detection ◽  
Control Chart ◽  
Biological Systems ◽  
Sum Of Squares ◽  
Data Driven ◽  
Model Based ◽  
Ewma Control Chart

scholarly journals A Gauge model-based analysis of: Reduction(s) in osmolyte infusion interval and its effects on the aggregate measure of systemic failure for a unicellular system

2015 ◽  
Author(s):  
Imadol V Jeff-Eke
Keyword(s):  
Biological Systems ◽  
Theoretical Problem ◽  
Gauge Model ◽  
Intracellular Space ◽  
Limited Availability ◽  
Model Based ◽  
Model Based Analysis ◽  
Aggregate Measure

This is a companion to A Gauge model for analysis of Biological systems. Here we reconcile the gauge model with a “real” system, which in this case is a unicellular system. We address effects of infusion of free osmolytes into an intracellular space of interest, and how changes to the frequency of infusion affects the aggregate measure of systemic failure. We also describe limitations to the functionality of the system that may stem from a limited availability of resources. We end by introducing a theoretical problem related to how well the system can tolerate random and extreme changes to the frequency of osmolytes presented via infusion.

scholarly journals A Gauge model-based analysis of: Reduction(s) in osmolyte infusion interval and its effects on the aggregate measure of systemic failure for a unicellular system

2015 ◽  
Author(s):  
Imadol V Jeff-Eke
Keyword(s):  
Biological Systems ◽  
Theoretical Problem ◽  
Gauge Model ◽  
Intracellular Space ◽  
Limited Availability ◽  
Model Based ◽  
Model Based Analysis ◽  
Aggregate Measure

This is a companion to A Gauge model for analysis of Biological systems. Here we reconcile the gauge model with a “real” system, which in this case is a unicellular system. We address effects of infusion of free osmolytes into an intracellular space of interest, and how changes to the frequency of infusion affects the aggregate measure of systemic failure. We also describe limitations to the functionality of the system that may stem from a limited availability of resources. We end by introducing a theoretical problem related to how well the system can tolerate random and extreme changes to the frequency of osmolytes presented via infusion.

A Gaussian mixture model based cost function for parameter estimation of chaotic biological systems

2015 ◽  
Vol 20 (2) ◽  
pp. 469-481 ◽  
Author(s):  
Yasser Shekofteh ◽  
Sajad Jafari ◽  
Julien Clinton Sprott ◽  
S. Mohammad Reza Hashemi Golpayegani ◽  
Farshad Almasganj
Keyword(s):  
Parameter Estimation ◽  
Cost Function ◽  
Gaussian Mixture Model ◽  
Mixture Model ◽  
Biological Systems ◽  
Gaussian Mixture ◽  
Model Based

Representation, abstraction, and simple-minded sophisticates

2020 ◽  
Vol 43 ◽  
Author(s):  
Peter Dayan
Keyword(s):  
Decision Theory ◽  
Predictive Coding ◽  
Bayesian Decision Theory ◽  
Bayesian Decision ◽  
Model Based ◽  
Model Free

Abstract Bayesian decision theory provides a simple formal elucidation of some of the ways that representation and representational abstraction are involved with, and exploit, both prediction and its rather distant cousin, predictive coding. Both model-free and model-based methods are involved.

Transmission Electron Microscopy of Protein Macromolecules

1971 ◽  
Vol 29 ◽  
pp. 424-425
Author(s):  
Henry S. Slayter
Keyword(s):  
Biological Systems ◽  
Metal Vapor ◽  
Resolving Power ◽  
Electron Microscopic ◽  
Chemical Methods ◽  
Molecular Weights ◽  
The Past ◽  
Physical Chemical ◽  
Transmission Electron

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.

Freeze-fracture cytochemistry: A goal set by Russell Steere in 1957

1993 ◽  
Vol 51 ◽  
pp. 60-61
Author(s):  
Nicholas J Severs
Keyword(s):  
Chemical Nature ◽  
Biological Systems ◽  
Freeze Fracture ◽  
Structural Components ◽  
Major Goal ◽  
Membrane Biology ◽  
Routine Application ◽  
The Future ◽  
Freeze Etching

In his pioneering demonstration of the potential of freeze-etching in biological systems, Russell Steere assessed the future promise and limitations of the technique with remarkable foresight. Item 2 in his list of inherent difficulties as they then stood stated “The chemical nature of the objects seen in the replica cannot be determined”. This defined a major goal for practitioners of freeze-fracture which, for more than a decade, seemed unattainable. It was not until the introduction of the label-fracture-etch technique in the early 1970s that the mould was broken, and not until the following decade that the full scope of modern freeze-fracture cytochemistry took shape. The culmination of these developments in the 1990s now equips the researcher with a set of effective techniques for routine application in cell and membrane biology.Freeze-fracture cytochemical techniques are all designed to provide information on the chemical nature of structural components revealed by freeze-fracture, but differ in how this is achieved, in precisely what type of information is obtained, and in which types of specimen can be studied.

Quantitative Model-Based Image Analysis of NuMa Distribution Links Nuclear Organization with Cell Phenotype

2001 ◽  
Vol 7 (S2) ◽  
pp. 578-579
Author(s):  
David W. Knowles ◽  
Sophie A. Lelièvre ◽  
Carlos Ortiz de Solόrzano ◽  
Stephen J. Lockett ◽  
Mina J. Bissell ◽  
...  
Keyword(s):  
Image Analysis ◽  
Mammary Epithelial Cells ◽  
Nuclear Organization ◽  
Critical Role ◽  
Quantitative Model ◽  
Mammary Epithelial ◽  
Cell Phenotype ◽  
Proliferating Cells ◽  
Mitotic Apparatus ◽  
Model Based

The extracellular matrix (ECM) plays a critical role in directing cell behaviour and morphogenesis by regulating gene expression and nuclear organization. Using non-malignant (S1) human mammary epithelial cells (HMECs), it was previously shown that ECM-induced morphogenesis is accompanied by the redistribution of nuclear mitotic apparatus (NuMA) protein from a diffuse pattern in proliferating cells, to a multi-focal pattern as HMECs growth arrested and completed morphogenesis . A process taking 10 to 14 days.To further investigate the link between NuMA distribution and the growth stage of HMECs, we have investigated the distribution of NuMA in non-malignant S1 cells and their malignant, T4, counter-part using a novel model-based image analysis technique. This technique, based on a multi-scale Gaussian blur analysis (Figure 1), quantifies the size of punctate features in an image. Cells were cultured in the presence and absence of a reconstituted basement membrane (rBM) and imaged in 3D using confocal microscopy, for fluorescently labeled monoclonal antibodies to NuMA (fαNuMA) and fluorescently labeled total DNA.

Sign in / Sign up

Export Citation Format

Share Document