Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Writing, Proofreading and Editing in Information Theory.

ABSTRACT: Information is a physical entity amenable to be described by an abstract theory. The concepts associated with the creation and post-processing of the information have not, however, been mathematically established, despite being broadly used in many fields of knowledge. Here, inspired by how information is managed in biomolecular systems, we introduce writing, entailing any bit string generation, and revision, as comprising proofreading and editing, in information chains. Our formalism expands the thermodynamic analysis of stochastic chains made up of material subunits to abstract strings of symbols. We introduce a non-Markovian treatment of operational rules over the symbols of the chain that parallels the physical interactions responsible for memory effects in material chains. Our theory underlies any communication system, ranging from human languages and computer science to gene evolution.

SUBMITTER: Arias-Gonzalez JR

PROVIDER: S-EPMC7512888 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Writing, Proofreading and Editing in Information Theory.

Arias-Gonzalez J Ricardo JR

Entropy (Basel, Switzerland) 20180515 5

Information is a physical entity amenable to be described by an abstract theory. The concepts associated with the creation and post-processing of the information have not, however, been mathematically established, despite being broadly used in many fields of knowledge. Here, inspired by how information is managed in biomolecular systems, we introduce writing, entailing any bit string generation, and revision, as comprising proofreading and editing, in information chains. Our formalism expands th ...[more]

PMID: 33265458

Similar Datasets

Main Ingredients for Success in L2 Academic Writing: Outlining, Drafting and Proofreading.

Project description:Spanish undergraduates of English Studies are required to submit their essays in academic English, a genre which most of them are not acquainted with. This paper aims to explore the extralinguistic side of second language (L2) academic writing, more specifically, the combination of metalinguistic items (e.g. transition and frame markers, among others) with students' writing strategies when composing an academic text in L2 English. The research sample conveys a group of 200 Spanish undergraduates of English Studies; they are in their fourth year, so they are expected to be proficient in English academic writing but their written production quality varies considerably. Results are analysed following a mixed methodology by which metalinguistic items are statistically measured, and then contrasted with semi-structured interview results; SPSS and NVivo provide quantitative and qualitative outcomes, respectively. The analyses reveal that undergraduate students who produce complex sentences and more coherent texts employ a wider range of writing strategies both prior and while writing, being able to (un)consciously structure and design their texts more successfully. These high-scoring students make more proficient use of complex transition markers for coherence and frame markers for textual cohesion; their commonly used (pre-)writing strategies are drafting, outlining, and proofreading.

| S-EPMC4457904 | biostudies-literature

Dissecting and tuning primer editing by proofreading polymerases.

Project description:Proofreading polymerases have 3' to 5' exonuclease activity that allows the excision and correction of mis-incorporated bases during DNA replication. In a previous study, we demonstrated that in addition to correcting substitution errors and lowering the error rate of DNA amplification, proofreading polymerases can also edit PCR primers to match template sequences. Primer editing is a feature that can be advantageous in certain experimental contexts, such as amplicon-based microbiome profiling. Here we develop a set of synthetic DNA standards to report on primer editing activity and use these standards to dissect this phenomenon. The primer editing standards allow next-generation sequencing-based enzymological measurements, reveal the extent of editing, and allow the comparison of different polymerases and cycling conditions. We demonstrate that proofreading polymerases edit PCR primers in a concentration-dependent manner, and we examine whether primer editing exhibits any sequence specificity. In addition, we use these standards to show that primer editing is tunable through the incorporation of phosphorothioate linkages. Finally, we demonstrate the ability of primer editing to robustly rescue the drop-out of taxa with 16S rRNA gene-targeting primer mismatches using mock communities and human skin microbiome samples.

| S-EPMC8421222 | biostudies-literature

Immune Literacy: Reading, Writing, and Editing Adaptive Immunity.

Project description:Advances in reading, writing, and editing DNA are providing unprecedented insights into the complexity of immunological systems. This combination of systems and synthetic biology methods is enabling the quantitative and precise understanding of molecular recognition in adaptive immunity, thus providing a framework for reprogramming immune responses for translational medicine. In this review, we will highlight state-of-the-art methods such as immune repertoire sequencing, immunoinformatics, and immunogenomic engineering and their application toward adaptive immunity. We showcase novel and interdisciplinary approaches that have the promise of transforming the design and breadth of molecular and cellular immunotherapies.

| S-EPMC7462589 | biostudies-literature

Information theory of metasurfaces.

Project description:We propose a theory to characterize the information and information processing abilities of metasurfaces, and demonstrate the relation between the information of the metasurface and its radiation pattern in the far-field region. By incorporating a general aperture model with uncertainty relation in L 2-space, we propose a theory to predict the upper bound of information contained in the radiation pattern of a metasurface, and reveal the theoretical upper limit of orthogonal radiation states. The proposed theory also provides guidance for inverse design of the metasurface with respect to given functionalities. Through investigation of the information of disordered-phase modulated metasurfaces, we find the information invariance (1-γ, where γ is Euler's constant) of chaotic radiation patterns. That is to say, the information of the disordered-phase modulated radiation patterns is always equal to 1-γ, regardless of variations in size, the number of elements and the phase pattern of metasurface. This value might be the lower bound of radiation-pattern information of the metasurface, which can provide a theoretical limit for information modulation applications, including computational imaging, stealth technologies and wireless communications.

| S-EPMC8289013 | biostudies-literature

Writing and erasing multicolored information in diarylethene-based supramolecular gels.

Project description:A facile cocktail approach implying the mixing of diarylethene (DAE) photoswitches and low molecular weight gelators (LMWG) is presented. The photoresponsive gels exhibit multicolored emission that can be precisely controlled by different light exposure schemes (wavelength and dose), applicable for fluorescence patterning/writing. Including also a blue-emitting fluorophore allows for tri-chromatic color tuning of the emission via multistep energy transfer reactions, which in turn yields a non-linear response between the emission spectra and the light dose. This feature is highly desired in data security and anti-counterfeiting contexts. The information written in the gels can be conveniently erased by light, mass diffusion, or shaking; the latter being due to the thixotropic properties of the gels.

| S-EPMC6202928 | biostudies-literature

Scaling theory for information networks.

Project description:Networks distribute energy, materials and information to the components of a variety of natural and human-engineered systems, including organisms, brains, the Internet and microprocessors. Distribution networks enable the integrated and coordinated functioning of these systems, and they also constrain their design. The similar hierarchical branching networks observed in organisms and microprocessors are striking, given that the structure of organisms has evolved via natural selection, while microprocessors are designed by engineers. Metabolic scaling theory (MST) shows that the rate at which networks deliver energy to an organism is proportional to its mass raised to the 3/4 power. We show that computational systems are also characterized by nonlinear network scaling and use MST principles to characterize how information networks scale, focusing on how MST predicts properties of clock distribution networks in microprocessors. The MST equations are modified to account for variation in the size and density of transistors and terminal wires in microprocessors. Based on the scaling of the clock distribution network, we predict a set of trade-offs and performance properties that scale with chip size and the number of transistors. However, there are systematic deviations between power requirements on microprocessors and predictions derived directly from MST. These deviations are addressed by augmenting the model to account for decentralized flow in some microprocessor networks (e.g. in logic networks). More generally, we hypothesize a set of constraints between the size, power and performance of networked information systems including transistors on chips, hosts on the Internet and neurons in the brain.

| S-EPMC2607348 | biostudies-literature

Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases.

Project description:Genome editing technologies that install diverse edits can widely enable genetic studies and new therapeutics. Here we develop click editing, a genome writing platform that couples the advantageous properties of DNA-dependent DNA polymerases with RNA-programmable nickases (e.g. CRISPR-Cas) to permit the installation of a range of edits including substitutions, insertions, and deletions. Click editors (CEs) leverage the "click"-like bioconjugation ability of HUH endonucleases (HUHes) with single stranded DNA substrates to covalently tether "click DNA" (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs (DNA polymerase and HUHe orthologs, architectural modifications, etc.) and their clkDNAs (template configurations, repair evading substitutions, etc.), we demonstrate the ability to install precise genome edits with minimal indels and no unwanted byproduct insertions. Since clkDNAs can be ordered as simple DNA oligonucleotides for cents per base, it is possible to screen many different clkDNA parameters rapidly and inexpensively to maximize edit efficiency. Together, click editing is a precise and highly versatile platform for modifying genomes with a simple workflow and broad utility across diverse biological applications.

| S-EPMC10515857 | biostudies-literature

Online peer editing: effects of comments and edits on academic writing skills.

Project description:Although the effects of online peer editing have been studied from a number of perspectives, it remains unclear how giving and receiving comments and edits affect student academic writing performance. The current study examined the influence of these aspects of peer editing on student academic writing performance in higher education during online peer editing. Participants were 76 students engaged in peer editing of one another's work in a graduate scientific writing course at a Korean university. The relationships between the giving and receiving of comments and edits, and student performance on their writing tasks were analyzed. Results showed that there is a positive correlation between the number of comments received and the student's writing score, whereas receiving edits had the opposite effect and was associated with lower student performance. Furthermore, no relationship was found between giving comments or edits and writing performance. These results add to the field's understanding of how specific elements of peer editing can impact students' performance.

| S-EPMC9254337 | biostudies-literature

Information theory, evolutionary innovations and evolvability.

Project description:How difficult is it to 'discover' an evolutionary adaptation or innovation? I here suggest that information theory, in combination with high-throughput DNA sequencing, can help answer this question by quantifying a new phenotype's information content. I apply this framework to compute the phenotypic information associated with novel gene regulation and with the ability to use novel carbon sources. The framework can also help quantify how DNA duplications affect evolvability, estimate the complexity of phenotypes and clarify the meaning of 'progress' in Darwinian evolution.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.

| S-EPMC5665804 | biostudies-literature

Perturbation Theory for the Information Bottleneck.

Project description:Extracting relevant information from data is crucial for all forms of learning. The information bottleneck (IB) method formalizes this, offering a mathematically precise and conceptually appealing framework for understanding learning phenomena. However the nonlinearity of the IB problem makes it computationally expensive and analytically intractable in general. Here we derive a perturbation theory for the IB method and report the first complete characterization of the learning onset-the limit of maximum relevant information per bit extracted from data. We test our results on synthetic probability distributions, finding good agreement with the exact numerical solution near the onset of learning. We explore the difference and subtleties in our derivation and previous attempts at deriving a perturbation theory for the learning onset and attribute the discrepancy to a flawed assumption. Our work also provides a fresh perspective on the intimate relationship between the IB method and the strong data processing inequality.

| S-EPMC9806839 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data