scholarly journals Selective Phenome Growth Adapted NK Model: A Novel Landscape to Represent Aptamer Ligand Binding

Complexity ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Andrew Brian Kinghorn ◽  
Julian Alexander Tanner
Keyword(s):  
Ligand Binding ◽  
Microarray Data ◽  
Computational Analysis ◽  
Selection Process ◽  
Theoretical Models ◽  
Fitness Landscapes ◽  
New Approach ◽  
Aptamer Selection ◽  
Interaction Map ◽  
Target Binding

Aptamers are single-stranded oligonucleotides selected by evolutionary approaches from massive libraries with significant potential for specific molecular recognition in diagnostics and therapeutics. A complete empirical characterisation of an aptamer selection experiment is not feasible due to the vast complexity of aptamer selection. Simulation of aptamer selection has been used to characterise and optimise the selection process; however, the absence of a good model for aptamer-target binding limits this field of study. Here, we generate theoretical fitness landscapes which appear to more accurately represent aptamer-target binding. The method used to generate these landscapes, selective phenome growth, is a new approach in which phenotypic contributors are added to a genotype/phenotype interaction map sequentially in such a way so as to increase the fitness of a selected fit sequence. In this way, a landscape is built around the selected fittest sequences. Comparison to empirical aptamer microarray data shows that our theoretical fitness landscapes more accurately represent aptamer ligand binding than other theoretical models. These improved fitness landscapes have potential for the computational analysis and optimisation of other complex systems.

scholarly journals Capillary transfer of soft films

2020 ◽  
Vol 117 (10) ◽  
pp. 5210-5216 ◽  
Author(s):  
Yue Zhang ◽  
Mengtian Yin ◽  
Yongmin Baek ◽  
Kyusang Lee ◽  
Giovanni Zangari ◽  
...  
Keyword(s):  
High Speed ◽  
Computational Analysis ◽  
Liquid Surface ◽  
Theoretical Models ◽  
Dynamic Contact ◽  
Surface Wetting ◽  
Motion Direction ◽  
Wetting Properties ◽  
Geometric Patterns ◽  
Solid Substrates

Existing transfer technologies in the construction of film-based electronics and devices are deeply established in the framework of native solid substrates. Here, we report a capillary approach that enables a fast, robust, and reliable transfer of soft films from liquid in a defect-free manner. This capillary transfer is underpinned by the transfer front of dynamic contact among receiver substrate, liquid, and film, and can be well controlled by a selectable motion direction of receiver substrates at a high speed. We demonstrate in extensive experiments, together with theoretical models and computational analysis, the robust capabilities of the capillary transfer using a versatile set of soft films with a broad material diversity of both film and liquid, surface-wetting properties, and complex geometric patterns of soft films onto various solid substrates in a deterministic manner.

scholarly journals Roles of cell and microvillus deformation and receptor-ligand binding kinetics in cell rolling

2008 ◽  
Vol 295 (4) ◽  
pp. H1439-H1450 ◽  
Author(s):  
Parag Pawar ◽  
Sameer Jadhav ◽  
Charles D. Eggleton ◽  
Konstantinos Konstantopoulos
Keyword(s):  
Ligand Binding ◽  
Three Dimensional ◽  
Theoretical Models ◽  
Binding Kinetics ◽  
Cell Deformation ◽  
Receptor Ligand ◽  
Length Scales ◽  
Bond Behavior ◽  
Cell Rolling ◽  
Threshold Phenomenon

Polymorphonuclear leukocyte (PMN) recruitment to sites of inflammation is initiated by selectin-mediated PMN tethering and rolling on activated endothelium under flow. Cell rolling is modulated by bulk cell deformation (mesoscale), microvillus deformability (microscale), and receptor-ligand binding kinetics (nanoscale). Selectin-ligand bonds exhibit a catch-slip bond behavior, and their dissociation is governed not only by the force but also by the force history. Whereas previous theoretical models have studied the significance of these three “length scales” in isolation, how their interplay affects cell rolling has yet to be resolved. We therefore developed a three-dimensional computational model that integrates the aforementioned length scales to delineate their relative contributions to PMN rolling. Our simulations predict that the catch-slip bond behavior and to a lesser extent bulk cell deformation are responsible for the shear threshold phenomenon. Cells bearing deformable rather than rigid microvilli roll slower only at high P-selectin site densities and elevated levels of shear (≥400 s−1). The more compliant cells (membrance stiffness = 1.2 dyn/cm) rolled slower than cells with a membrane stiffness of 3.0 dyn/cm at shear rates >50 s−1. In summary, our model demonstrates that cell rolling over a ligand-coated surface is a highly coordinated process characterized by a complex interplay between forces acting on three distinct length scales.

Dynamical versus isolated formation channels of gravitational wave sources

2018 ◽  
Vol 14 (S346) ◽  
pp. 397-416
Author(s):  
Michela Mapelli
Keyword(s):  
Black Holes ◽  
Neutron Stars ◽  
Gravitational Wave ◽  
Theoretical Models ◽  
Stellar Winds ◽  
Core Collapse ◽  
Dynamical Processes ◽  
New Approach ◽  
The Impact

AbstractWhat are the formation channels of merging black holes and neutron stars? The first two observing runs of Advanced LIGO and Virgo give us invaluable insights to address this question, but a new approach to theoretical models is required, in order to match the challenges posed by the new data. In this review, I discuss the impact of stellar winds, core-collapse and pair instability supernovae on the formation of compact remnants in both isolated and dynamically formed binaries. Finally, I show that dynamical processes, such as the runaway collision scenario and the Kozai-Lidov mechanism, leave a clear imprint on the demography of merging systems.

Vector space model for patent documents with hierarchical class labels

2012 ◽  
Vol 38 (3) ◽  
pp. 222-233 ◽  
Author(s):  
Yen-Liang Chen ◽  
Yu-Ting Chiu
Keyword(s):  
Feature Selection ◽  
Vector Space ◽  
Selection Process ◽  
Vector Space Model ◽  
Class Label ◽  
Discriminative Ability ◽  
New Approach ◽  
Space Model ◽  
Patent Documents ◽  
Class Labels

A vector space model (VSM) composed of selected important features is a common way to represent documents, including patent documents. Patent documents have some special characteristics that make it difficult to apply traditional feature selection methods directly: (a) it is difficult to find common terms for patent documents in different categories; and (b) the class label of a patent document is hierarchical rather than flat. Hence, in this article we propose a new approach that includes a hierarchical feature selection (HFS) algorithm which can be used to select more representative features with greater discriminative ability to present a set of patent documents with hierarchical class labels. The performance of the proposed method is evaluated through application to two documents sets with 2400 and 9600 patent documents, where we extract candidate terms from their titles and abstracts. The experimental results reveal that a VSM whose features are selected by a proportional selection process gives better coverage, while a VSM whose features are selected with a weighted-summed selection process gives higher accuracy.

Computational analysis of microarray data

2001 ◽  
Vol 2 (6) ◽  
pp. 418-427 ◽  
Author(s):  
John Quackenbush
Keyword(s):  
Microarray Data ◽  
Computational Analysis

Study on the Method of Isolating the Aptamer from the Surface of HepG2 Cells

2020 ◽  
Vol 20 (6) ◽  
pp. 3373-3377 ◽  
Author(s):  
Zhukang Guo ◽  
Chao Wang ◽  
Song Li ◽  
Zhu Chen ◽  
Yan Deng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Malignant Tumor ◽  
Hepg2 Cells ◽  
Early Stage ◽  
Selection Process ◽  
Carcinoma Cells ◽  
Ultrapure Water ◽  
Aptamer Selection ◽  
Fluorescent Pcr ◽  
Automated Instrument

The hepatocellular carcinoma (HCC) is a malignant tumor that occurs in the liver. It is a common malignant tumor in clinic. The main reason for its high mortality is its early latency. Therefore, how to accurately determine and test the hepatocellular carcinoma in the early stage has a very positive significance for the treatment. It is an important method for the early diagnosis of the hepatocellular carcinoma to use aptamers specifically binding to hepatocellular carcinoma cells, which has good application prospects. In order to improve the efficiency of aptamer selection of tumor cells, our group designed and developed an automated instrument for the aptamer selection. In this paper, the method to separate bound aptamers from the surface of HepG2 cells in automated selection process was studied, and the feasibility of separating binding aptamers from the HepG2 cell surface using ultrapure water and the effect of different temperature environments on its isolation were discussed. Results of the real-time fluorescent PCR and flow cytometry showed that ultrapure water could be used to isolate bound HepG2 cells and aptamers, and the concentration of the aptamers increased with the rise of the temperature between 25 and 80 degrees Celsius. This result will contribute to the improvement on the efficiency of automated selections for aptamers corresponding to HepG2 cells.

Triple-Choking Model for Ejector

2010 ◽  
Vol 2 (2) ◽  
Author(s):  
J. Sargolzaei ◽  
M. R. Pirzadi Jahromi ◽  
E. Saljoughi
Keyword(s):  
Theoretical Models ◽  
Mixing Efficiency ◽  
Governing Equations ◽  
Critical Mode ◽  
Cross Sectional ◽  
New Approach ◽  
Mode Operation ◽  
Operation Conditions ◽  
Mixing Chamber ◽  
Good Agreement

In this study, a 1D analysis has been presented for the prediction of ejector performance at critical mode operation. The new triple-choking model has been developed using the governing equations of the compressible fluids and thermodynamics properties based on the frictional adiabatic fluid study. A new approach has been introduced to consider the frictional effects on the mixing efficiencies by extending the 1D ejector theory. A very good agreement has been reported for the R141b and steam experimental data at critical mode operation. Furthermore, simulated results have been compared with some of the recent theoretical models. In addition, the influence of operation conditions on the ejector performance and the required cross-sectional area of the mixing chamber has been showed. Finally, the influence of the operation conditions (such as generator, condenser, and evaporator temperatures) and the size of ejector on the mixing efficiency have been studied.

Television's Role in Family Interaction

1983 ◽  
Vol 4 (2) ◽  
pp. 405-424 ◽  
Author(s):  
IRENE F. GOODMAN
Keyword(s):  
Family Systems ◽  
Measurement Techniques ◽  
Theoretical Models ◽  
Future Research ◽  
New Approach ◽  
Systems Model ◽  
Television Use ◽  
The Family ◽  
Shed Light

The purpose of this article is to argue that exploring the role of television in family life is not solely a matter of studying its effects on family members; it also involves looking at TV as a phenomenon that serves a whole range of social purposes the study of which can shed light on general family functioning. In this review, existing theoretical models and research are discussed in order to show why a new model—family systems—is being proposed. The application of the family systems model to the arena of television use in the family is one that has not been previously explored. Emphasis will be placed on two family systems principles that are important in the study of the family's use of and interaction around television. Current measurement techniques will be examined to illustrate that a new approach, reflecting interaction and process, is needed. Components of a family systems model—structure, development, and adaptation—are adapted in order to discuss TV's function in the family. Suggestions for future research and implications for therapy are offered.

Price for Opening the Transient Specificity Pocket in Human Aldose Reductase upon Ligand Binding: Structural, Thermodynamic, Kinetic, and Computational Analysis

2017 ◽  
Vol 12 (5) ◽  
pp. 1397-1415 ◽  
Author(s):  
Chris Rechlin ◽  
Frithjof Scheer ◽  
Felix Terwesten ◽  
Tobias Wulsdorf ◽  
Ewa Pol ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Aldose Reductase ◽  
Computational Analysis
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