Search results for "CODE"
showing 10 items of 1180 documents
3-dimensional Analysis and Literature Review of the Root Canal Morphology and Physiological Foramen Geometry of 125 Mandibular Incisors by Means of M…
2019
Abstract Introduction The aim of this study was to examine the root canal system morphology of mandibular incisors by means of micro–computed tomographic imaging. Methods The root canal configuration, physiological foramina, frequency of accessory and connecting canals, and the size and shape of the physiological foramina of 125 mandibular incisors were investigated by means of micro-CT and 3-dimensional imaging software. Root canal configuration of the coronal, middle, and apical thirds and the physiological foramina number are described by a 4-digit system code. Results The most frequent root canal configurations were 1-1-1/1 (56%), 1-2-1/1 (17.6%), and 1-1-1/2 (10.4%); 9 additional diffe…
Identification of control targets in Boolean molecular network models via computational algebra
2015
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The pot…
Modern diversification of the amino acid repertoire driven by oxygen
2017
All extant life employs the same 20 amino acids for protein biosynthesis. Studies on the number of amino acids necessary to produce a foldable and catalytically active polypeptide have shown that a basis set of 7-13 amino acids is sufficient to build major structural elements of modern proteins. Hence, the reasons for the evolutionary selection of the current 20 amino acids out of a much larger available pool have remained elusive. Here, we have analyzed the quantum chemistry of all proteinogenic and various prebiotic amino acids. We find that the energetic HOMO-LUMO gap, a correlate of chemical reactivity, becomes incrementally closer in modern amino acids, reaching the level of specialize…
MultiBacTAG-Genetic Code Expansion Using the Baculovirus Expression System in Sf21 Cells
2018
The combination of genetic code expansion (GCE) and baculovirus-based protein expression in Spodoptera frugiperda cells is a powerful tool to express multiprotein complexes with site-specifically introduced noncanonical amino acids. This protocol describes the integration of synthetase and tRNA gene indispensable for GCE into the backbone of the Bacmid, the Tn7-mediated transposition of various genes of interest, as well as the final expression of protein using the MultiBacTAG system with different noncanonical amino acids.
Graphical Workflow System for Modification Calling by Machine Learning of Reverse Transcription Signatures
2019
Modification mapping from cDNA data has become a tremendously important approach in epitranscriptomics. So-called reverse transcription signatures in cDNA contain information on the position and nature of their causative RNA modifications. Data mining of, e.g. Illumina-based high-throughput sequencing data, is therefore fast growing in importance, and the field is still lacking effective tools. Here we present a versatile user-friendly graphical workflow system for modification calling based on machine learning. The workflow commences with a principal module for trimming, mapping, and postprocessing. The latter includes a quantification of mismatch and arrest rates with single-nucleotide re…
Environmental epigenetics in zebrafish
2017
Abstract It is widely accepted that the epigenome can act as the link between environmental cues, both external and internal, to the organism and phenotype by converting the environmental stimuli to phenotypic responses through changes in gene transcription outcomes. Environmental stress endured by individual organisms can also enforce epigenetic variations in offspring that had never experienced it directly, which is termed transgenerational inheritance. To date, research in the environmental epigenetics discipline has used a wide range of both model and non-model organisms to elucidate the various epigenetic mechanisms underlying the adaptive response to environmental stimuli. In this rev…
Drosophila Food-Associated Pheromones: Effect of Experience, Genotype and Antibiotics on Larval Behavior
2016
International audience; Animals ubiquitously use chemical signals to communicate many aspects of their social life. These chemical signals often consist of environmental cues mixed with species-specific signals-pheromones-emitted by conspecifics. During their life, insects can use pheromones to aggregate, disperse, choose a mate, or find the most suitable food source on which to lay eggs. Before pupariation, larvae of several Drosophila species migrate to food sources depending on their composition and the presence of pheromones. Some pheromones derive from microbiota gut activity and these food-associated cues can enhance larval attraction or repulsion. To explore the mechanisms underlying…
Statistical Explorations and Univariate Timeseries Analysis on COVID-19 Datasets to Understand the Trend of Disease Spreading and Death
2020
&ldquo
Towards identifying drug side effects from social media using active learning and crowd sourcing.
2019
Motivation Social media is a largely untapped source of information on side effects of drugs. Twitter in particular is widely used to report on everyday events and personal ailments. However, labeling this noisy data is a difficult problem because labeled training data is sparse and automatic labeling is error-prone. Crowd sourcing can help in such a scenario to obtain more reliable labels, but is expensive in comparison because workers have to be paid. To remedy this, semi-supervised active learning may reduce the number of labeled data needed and focus the manual labeling process on important information. Results We extracted data from Twitter using the public API. We subsequently use Ama…
An optimal population code for global motion estimation in local direction-selective cells
2021
AbstractNervous systems allocate computational resources to match stimulus statistics. However, the physical information that needs to be processed depends on the animal’s own behavior. For example, visual motion patterns induced by self-motion provide essential information for navigation. How behavioral constraints affect neural processing is not known. Here we show that, at the population level, local direction-selective T4/T5 neurons in Drosophila represent optic flow fields generated by self-motion, reminiscent to a population code in retinal ganglion cells in vertebrates. Whereas in vertebrates four different cell types encode different optic flow fields, the four uniformly tuned T4/T5…