scholarly journals Invasion performance-similarity found among multiple cell systems

2020 ◽  
Author(s):  
Om Prakash

ABSTRACTUnderstanding of inter-system behavior develops biologically relevant intuition for drug repositioning as well as other biological research. But combining all the possible genes interactions into a system, and furthermore comparisons of multiple systems are a challenge on time ground with feasible experiments. In present study, 64 cell lines from 11 different organs were compared for their invasion performance. RNA expressions of 23 genes were used to create systems artificial neural network (ANN) models. ANN models were prepared for all 64 cell lines and observed for their invasion performance through network mapping. The resulted cell line clusters bear feasible capacity to perform experiments for biologically relevant research motivations as drug repositioning and selective targeting etc.; and can be used for analysis of invasion related aspects.

Metabolomics ◽  
2020 ◽  
Vol 16 (10) ◽  
Author(s):  
Marina Wright Muelas ◽  
Ivayla Roberts ◽  
Farah Mughal ◽  
Steve O’Hagan ◽  
Philip J. Day ◽  
...  

Abstract Introduction It is widely but erroneously believed that drugs get into cells by passing through the phospholipid bilayer portion of the plasma and other membranes. Much evidence shows, however, that this is not the case, and that drugs cross biomembranes by hitchhiking on transporters for other natural molecules to which these drugs are structurally similar. Untargeted metabolomics can provide a method for determining the differential uptake of such metabolites. Objectives Blood serum contains many thousands of molecules and provides a convenient source of biologically relevant metabolites. Our objective was to detect and identify metabolites present in serum, but to also establish a method capable of measure their uptake and secretion by different cell lines. Methods We develop an untargeted LC-MS/MS method to detect a broad range of compounds present in human serum. We apply this to the analysis of the time course of the uptake and secretion of metabolites in serum by several human cell lines, by analysing changes in the serum that represents the extracellular phase (the ‘exometabolome’ or metabolic footprint). Results Our method measures some 4000–5000 metabolic features in both positive and negative electrospray ionisation modes. We show that the metabolic footprints of different cell lines differ greatly from each other. Conclusion Our new, 15-min untargeted metabolome method allows for the robust and convenient measurement of differences in the uptake of serum compounds by cell lines following incubation in serum. This will enable future research to study these differences in multiple cell lines that will relate this to transporter expression, thereby advancing our knowledge of transporter substrates, both natural and xenobiotic compounds.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicola A. Thompson ◽  
Marco Ranzani ◽  
Louise van der Weyden ◽  
Vivek Iyer ◽  
Victoria Offord ◽  
...  

AbstractGenetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. Our studies reveal the fitness effects of FAM50A/FAM50B in cancer cells.


Metals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 729
Author(s):  
Junhyub Jeon ◽  
Namhyuk Seo ◽  
Hwi-Jun Kim ◽  
Min-Ha Lee ◽  
Hyun-Kyu Lim ◽  
...  

Fe-based bulk metallic glasses (BMGs) are a unique class of materials that are attracting attention in a wide variety of applications owing to their physical properties. Several studies have investigated and designed the relationships between alloy composition and thermal properties of BMGs using an artificial neural network (ANN). The limitation of the wide-scale use of these models is that the required composition is yet to be found despite numerous case studies. To address this issue, we trained an ANN to design Fe-based BMGs that predict the thermal properties. Models were trained using only the composition of the alloy as input and were created from a database of more than 150 experimental data of Fe-based BMGs from relevant literature. We adopted these ANN models to design BMGs with thermal properties to satisfy the intended purpose using particle swarm optimization. A melt spinner was employed to fabricate the designed alloys. X-ray diffraction and differential thermal analysis tests were used to evaluate the specimens.


2011 ◽  
Vol 6 (6) ◽  
pp. 514-522 ◽  
Author(s):  
C. McFadden ◽  
C. L. Mallett ◽  
P. J. Foster

2019 ◽  
Author(s):  
Jervis Vermal Thevathasan ◽  
Maurice Kahnwald ◽  
Konstanty Cieśliński ◽  
Philipp Hoess ◽  
Sudheer Kumar Peneti ◽  
...  

AbstractQuantitative fluorescence and superresolution microscopy are often limited by insufficient data quality or artifacts. In this context, it is essential to have biologically relevant control samples to benchmark and optimize the quality of microscopes, labels and imaging conditions.Here we exploit the stereotypic arrangement of proteins in the nuclear pore complex as in situ reference structures to characterize the performance of a variety of microscopy modalities. We created four genome edited cell lines in which we endogenously labeled the nucleoporin Nup96 with mEGFP, SNAP-tag or HaloTag or the photoconvertible fluorescent protein mMaple. We demonstrate their use a) as 3D resolution standards for calibration and quality control, b) to quantify absolute labeling efficiencies and c) as precise reference standards for molecular counting.These cell lines will enable the broad community to assess the quality of their microscopes and labels, and to perform quantitative, absolute measurements.


2021 ◽  
Author(s):  
DEVIN NIELSEN ◽  
TYLER LOTT ◽  
SOM DUTTA ◽  
JUHYEONG LEE

In this study, three artificial neural network (ANN) models are developed with back propagation (BP) optimization algorithms to predict various lightning damage modes in carbon/epoxy laminates. The proposed ANN models use three input variables associated with lightning waveform parameters (i.e., the peak current amplitude, rising time, and decaying time) to predict fiber damage, matrix damage, and through-thickness damage in the composites. The data used for training and testing the networks was actual lightning damage data collected from peer-reviewed published literature. Various BP training algorithms and network architecture configurations (i.e., data splitting, the number of neurons in a hidden layer, and the number of hidden layers) have been tested to improve the performance of the neural networks. Among the various BP algorithms considered, the Bayesian regularization back propagation (BRBP) showed the overall best performance in lightning damage prediction. When using the BRBP algorithm, as expected, the greater the fraction of the collected data that is allocated to the training dataset, the better the network is trained. In addition, the optimal ANN architecture was found to have a single hidden layer with 20 neurons. The ANN models proposed in this work may prove useful in preliminary assessments of lightning damage and reduce the number of expensive experimental lightning tests.


2016 ◽  
pp. 368-395
Author(s):  
Eliano Pessa

The Artificial Neural Network (ANN) models gained a wide popularity owing to a number of claimed advantages such as biological plausibility, tolerance with respect to errors or noise in the input data, learning ability allowing an adaptability to environmental constraints. Notwithstanding the fact that most of these advantages are not typical only of ANNs, engineers, psychologists and neuroscientists made an extended use of ANN models in a large number of scientific investigations. In most cases, however, these models have been introduced in order to provide optimization tools more useful than the ones commonly used by traditional Optimization Theory. Unfortunately, just the successful performance of ANN models in optimization tasks produced a widespread neglect of the true – and important – objectives pursued by the first promoters of these models. These objectives can be shortly summarized by the manifesto of connectionist psychology, stating that mental processes are nothing but macroscopic phenomena, emergent from the cooperative interaction of a large number of microscopic knowledge units. This statement – wholly in line with the goal of statistical mechanics – can be readily extended to other processes, beyond the mental ones, including social, economic, and, in general, organizational ones. Therefore this chapter has been designed in order to answer a number of related questions, such as: are the ANN models able to grant for the occurrence of this sort of emergence? How can the occurrence of this emergence be empirically detected? How can the emergence produced by ANN models be controlled? In which sense the ANN emergence could offer a new paradigm for the explanation of macroscopic phenomena? Answering these questions induces to focus the chapter on less popular ANNs, such as the recurrent ones, while neglecting more popular models, such as perceptrons, and on less used units, such as spiking neurons, rather than on McCulloch-Pitts neurons. Moreover, the chapter must mention a number of strategies of emergence detection, useful for researchers performing computer simulations of ANN behaviours. Among these strategies it is possible to quote the reduction of ANN models to continuous models, such as the neural field models or the neural mass models, the recourse to the methods of Network Theory and the employment of techniques borrowed by Statistical Physics, like the one based on the Renormalization Group. Of course, owing to space (and mathematical expertise) requirements, most mathematical details of the proposed arguments are neglected, and, to gain more information, the reader is deferred to the quoted literature.


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