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At least 1,063 records · Page 59

Unnatural reactive amino acid genetic code additions

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

59 BASIC BIOLOGICAL SCIENCES↗

Expanding the eukaryotic genetic code

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic Algorithms and Classification Trees in Feature Discovery: Diabetes and the NHANES database

This paper presents a feature selection methodology that can be applied to datasets containing a mixture of continuous and categorical variables. Using a Genetic Algorithm (GA), this method explores a dataset and selects a small set of features relevant for the prediction of a binary (1/0) response. Binary classification trees and an objective function based on conditional probabilities are used to measure the fitness of a given subset of features. The method is applied to health data in order to find factors useful for the prediction of diabetes. Results show that our algorithm is capable of narrowing down the set of predictors to around 8 factors that can be validated using reputable medical and public health resources.

Heredia-Langner, Alejandro↗

Utilizing Genetic Programming to Identify Failures in ICS Networks

Previously, researchers have attempted to apply machine learning techniques to network anomaly detection problems. Due to the staggering amount of variety that can occur in normal networks, the results have often been underwhelming. These challenges are far less pronounced when considering industrial control system (ICS) networks. The recurrent nature of these networks results in less noise and more consistent patterns for a machine learning algorithm to recognize. Here, we propose a method of evolving decision trees through genetic programming (GP) in order to detect network anomalies, such as device outages. Our approach extracts over a dozen features from network packet captures and netflows, normalizes them, and relates them in decision trees using fuzzy logic operators. Furthermore, the trees were used to detect three specific network events from three different points on the network across a statistically significant number of runs and achieved 100% accuracy on five of the nine experiments. When the trees attempted to detect more challenging events at points of presence further from the occurrence, the accuracy averaged to above 98%. Finally, using our method, all of the evolutionary cycles of the GP algorithm are computed a-priori, allowing the best resultant trees to be deployed as semi-real-time sensors with little overhead.

97 MATHEMATICS AND COMPUTING↗

Expanding the eukaryotic genetic code

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

59 BASIC BIOLOGICAL SCIENCES↗

Unnatural reactive amino acid genetic code additions

This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

59 BASIC BIOLOGICAL SCIENCES↗

Constructs and methods for genome editing and genetic engineering of fungi and protists

Provided herein are constructs for genome editing or genetic engineering in fungi or protists, methods of using the constructs and media for use in selecting cells. The construct include a polynucleotide encoding a thymidine kinase operably connected to a promoter, suitably a constitutive promoter; a polynucleotide encoding an endonuclease operably connected to an inducible promoter; and a recognition site for the endonuclease. The constructs may also include selectable markers for use in selecting recombinations.

59 BASIC BIOLOGICAL SCIENCES↗

Development Of A Novel Genetic Algorithm-based Optimization Method For Design Of Nuclear Criticality Experiments

A new evaluation of isotopic molybdenum total neutron cross section data based on measurements performed at Rensselaer Polytechnic Institute prompted researchers at Rensselaer and Los Alamos National Laboratory (LANL) to design a nuclear criticality experiment for the validation of the data. A novel approach of criticality experiment design employing a genetic algorithm-based optimization technique was developed. The method produced a critical experiment with a cross section sensitivity that exceeded target specifications by an order of magnitude.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic algorithm for demand response: a stackelberg game approach

Demand response (DR) has gained a significant recent interest due to its potential for mitigating many power system problems. Game theory is a very effective tool to be utilized in DR management. In this paper, the DR between a distribution system operator (DSO) and load aggregators (LAs) is designed as a Stackelberg game, where the DSO acts as the leader and LAs are regarded as the followers. Due to the limitations of the centralized solution approaches, a genetic algorithm-based decentralized approach is proposed. To demonstrate the proposed approach, a case study concerning a day-ahead optimization for a real-time pricing market with a single DSO and three LAs is designed and optimized. The proposed approach is able to shift the demand peaks and prove that it has a great potential to be used for the Stackelberg game between a DSO and multiple LAs to fully exploit the potential of DR.

Amasyali, Kadir↗

Constructs and methods for genome editing and genetic engineering of fungi and protists

Provided herein are constructs for genome editing or genetic engineering its fungi or protists, methods of using the constructs and media for use in selecting cells. The construct include a polynucleotide encoding a thymidine kinase operably connected to a promoter, suitably a constitutive promoter; a polynucleotide encoding an endonuclease operably connected to an inducible promoter; and a recognition site for the endonuclease. The constructs may also include selectable markers for use in selecting recombinations.

Hittinger, Christopher Todd↗

A reproducibility study of "Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space"

Nigam et al. reported a genetic algorithm (GA) utilizing the SELFIES representation and also propose an adaptive, neural network-based penalty that is supposed to improve the diversity of the generated molecules. The main claims of the paper are that this GA outperforms other generative techniques (as measured by the penalized logP) and that a neural network-based adaptive penalty increases the diversity of the generated molecules. In this work, we investigated the reproducibility of their claims. Overall, we were able to reproduce comparable results using the SELFIES-based GA, but mostly by exploiting deficiencies of the (easily optimizable) fitness function (i.e., generating long, sulfur containing chains). In addition, we reproduce results showing that the discriminator can be used to bias the generation of molecules to ones that are similar to the reference set. Lastly, we attempted to quantify the evolution of the diversity, understand the influence of some hyperparameters, and propose improvements to the adaptive penalty.

Jablonka, Kevin Maik↗

Engineering organisms resistant to viruses and horizontally transferred genetic elements

Organisms resistant to horizontal gene transfer (HGT), and compositions and methods of use thereof are provided. The organisms are typically genomically recoded organisms (GRO), typically cells, having a genome in which at least one endogenous codon has been eliminated by reassignment of the codon to a synonymous or non-synonymous codon. The GRO typically include a recombinant expression construct for expression of at least one element of a ribosomal rescue pathway, typically lacking the eliminated codon. Typically, the disclosed cells are resistant to completed transfer and/or expression of a horizontally transferred genetic element (HTGE) from another organism compared a corresponding cell having a genome wherein the eliminated codon has not been eliminated. In some embodiments, the organism from which the HTGE is being transferred is a bacterium or a virus.

Isaacs, Farren J.↗