Simplicity, function, and legibility in an enhanced ambigraphic nucleic acid notation

We previously showed that an ambigraphic nucleic acid notation, based on symmetrical lowercase Roman characters, permits users to complement DNA by physically rotating the sequence text 180 degrees . This article describes an enhanced ambigraphic notation, which uses concept-related symbol design, rather than the arbitrary set of symbols that constitute the Roman alphabet, to logically encode the four DNA bases and 11 ambiguity characters. As ambigrams, the symbols continue to permit the rapid derivation of complementary sequences and visualization of palindromic DNA. In addition, the new AmbiScript notation uses legibility principles to support the identification of sequence polymorphism and improves writing efficiency by requiring fewer strokes per character than the International Union of Pure and Applied Chemistry (IUPAC) notation.     

Towards a theory of the evolution of butterfly colour patterns under directional and disruptive selection

Two general models for the transspecific evolution of butterfly colour patterns are advanced: directional selection acting equally on both sexes, and disruptive selection involving periods of polymorphism. To consider possible outcomes of me latter process, a morphism notation based on an integrated classification for polymorphism and sexual dimorphism is developed. This notation is used to examine the properties of all morphism transformations possible from the minimal expressions of the nine morphism categories, as reached through defined minimum step changes. The significance of such pathway models is analysed in terms of general properties of butterfly polymorphism. The potential use of pathway models in evolutionary studies is briefly discussed, mainly with respect to phylogenetics, and ideas on the evolution of genetic dominance.     

The Practical and Pedagogical Advantages of an Ambigraphic Nucleic Acid Notation

The universally applied IUPAC notation for nucleic acids was adopted primarily to facilitate the mental association of G, A, T, C, and the related ambiguity characters with the bases they represent. However, it is possible to create a notation that offers greater support for the basic manipulations and analyses to which genetic sequences frequently are subjected. By designing a nucleic acid notation around ambigrams, it is possible to simplify the frequently applied process of reverse complementation and aid the visualization of palindromes. The ambigraphic notation presented here also uses common orthographic features such as stems and loops to highlight guanine and cytosine rich regions, support the derivation of ambiguity characters, and aid educators in teaching the fundamentals of molecular genetics.     

The practical and pedagogical advantages of an ambigraphic nucleic acid notation

The universally applied IUPAC notation for nucleic acids was adopted primarily to facilitate the mental association of G, A, T, C, and the related ambiguity characters with the bases they represent. However it is possible to create a notation that offers greater support for the basic manipulations and analyses to which genetic sequences frequently are subjected. By designing a nucleic acid notation around ambigrams, it is possible to simplify the frequently applied process of reverse complementation and aid the visualization of palindromes. The ambigraphic notation presented here also uses common orthographic features such as stems and loops to highlight guanine and cytosine rich regions, support the derivation of ambiguity characters, and aid educators in teaching the fundamentals of molecular genetics.     

The interpretation of selection coefficients

Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility—which allows different biological units to be identified as targets of selection—is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under “direct” versus “indirect” selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so.     

THE NOTATION OF BIRD-SONG:A REVIEW AND A RECOMMENDATION

The reasons for a systematic form of notation of bird-song are discussed. Though the sound spectrograph will remain the primary tool in any study of bird-vocalization, there is still a need for a simple, comprehensive notation for the bird-watcher. This will act as a supplement to the bird-song recordings now available. After a survey of various attempts at bird-notation, from syllabic notation to the sophisticated graph-methods suggested by Stadler & Schmitt, A. A. Saunders and Gladys Page-Wood, recommendations for a comprehensive notation are made, illustrated by notated examples of song-phrases from the Nightingale.     

Molecular interaction maps of bioregulatory networks: a general rubric for systems biology

A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become standard. We have prepared many detailed bioregulatory network diagrams using the molecular interaction map (MIM) notation, and we now feel confident that it is suitable as a standard. Here, we describe the MIM notation formally and discuss its merits relative to alternative proposals. We show by simple examples how to denote all of the molecular interactions commonly found in bioregulatory networks. There are two forms of MIM diagrams. "Heuristic" MIMs present the repertoire of interactions possible for molecules that are colocalized in time and place. "Explicit" MIMs define particular models (derived from heuristic MIMs) for computer simulation. We show also how pathways or processes can be highlighted on a canonical heuristic MIM. Drawing a MIM diagram, adhering to the rules of notation, imposes a logical discipline that sharpens one's understanding of the structure and function of a network.     

A 3D Generic Inverse Dynamic Method using Wrench Notation and Quaternion Algebra

In the literature, conventional 3D inverse dynamic models are limited in three aspects related to inverse dynamic notation, body segment parameters and kinematic formalism. First, conventional notation yields separate computations of the forces and moments with successive coordinate system transformations. Secondly, the way conventional body segment parameters are defined is based on the assumption that the inertia tensor is principal and the centre of mass is located between the proximal and distal ends. Thirdly, the conventional kinematic formalism uses Euler or Cardanic angles that are sequence-dependent and suffer from singularities.

In order to overcome these limitations, this paper presents a new generic method for inverse dynamics. This generic method is based on wrench notation for inverse dynamics, a general definition of body segment parameters and quaternion algebra for the kinematic formalism.     

A 3D generic inverse dynamic method using wrench notation and quaternion algebra

In the literature, conventional 3D inverse dynamic models are limited in three aspects related to inverse dynamic notation, body segment parameters and kinematic formalism. First, conventional notation yields separate computations of the forces and moments with successive coordinate system transformations. Secondly, the way conventional body segment parameters are defined is based on the assumption that the inertia tensor is principal and the centre of mass is located between the proximal and distal ends. Thirdly, the conventional kinematic formalism uses Euler or Cardanic angles that are sequence-dependent and suffer from singularities. In order to overcome these limitations, this paper presents a new generic method for inverse dynamics. This generic method is based on wrench notation for inverse dynamics, a general definition of body segment parameters and quaternion algebra for the kinematic formalism.     

A proposal for a convenient notation for P-chiral nucleotide analogues. Part 3. Compounds with one nucleoside residue and nonnucleosidic derivatives

Recently, we have proposed a new DP/LP stereochemical notation for P-chiral dinucleoside monophosphate analogues that permits simple correlation between spatial arrangement of the substituents and the configuration at the phosphorus center. As an extension of this work, we present here applications of the DP/LP notation to derivatives containing only one nucleoside unit (e.g., alkyl nucleoside phosphodiesters, nucleoside phosphomonoesters, cyclic phosphate derivatives, nucleoside di-, and triphosphates) and to nonnucleosidic phosphorus compounds.     

Assignment of the red cell antigen, Targett (Rh40), to the Rh blood group system.

Statistical and serological evidence from a large kindred and two unrelated adults indicates that Targett (Tar) is an antigen in the Rh blood group system and that its presence is assocciated with a weak expression of the Rh antigen D. In the numerical notation the Tar antigen is designated Rh40.     

Joint Report of the Fourth International Workshop on Lymphocyte Alloantigens of the Horse, Lexington, Kentucky, 12–22 October 1985

Summary. The workshop consisted of 12 monthly cell exchanges of full-sibling families among the 10 participating laboratories. A total of 33 parents, 52 offspring and five unrelated horses were typed by each laboratory using local antisera. The raw data were submitted for central analysis before any identification of the animals was revealed.
Confidence derived from the consistent agreement between the laboratories on the assignment and segregation of the first 10 ELA-W specificities led to the removal of the W (workshop) notation and acceptance of full status as locus A antigens. The seemingly supertypic W11 specificity, however, remained unchanged.
Ten additional specificities were seen to segregate with the ELA system, suggesting either splits of previously described specificities or products of linked loci. The workshop (W) notation was given to the 10 specificities W12-W21, befitting their status as specificities under study.
The previously described ELY-1.1 specificity, characterized by segregation independent from the ELA system, was confirmed along with a new specificity, ELY-1.2, which behaves as an allele of ELY-1.1. For informative families, the two specificities showed codominant expression and appeared to constitute a closed, autosomal system.
The ELY-2.1 specificity was confirmed to segregate independently from the ELA-A and ELY-1 loci.     

Vectorial capacity, basic reproduction number, force of infection and all that: formal notation to complete and adjust their classical concepts and equations

A dimensional analysis of the classical equations related to the dynamics of vector-borne infections is presented. It is provided a formal notation to complete the expressions for the Ross' Threshold Theorem, the Macdonald's basic reproduction "rate" and sporozoite "rate", Garret-Jones' vectorial capacity and Dietz-Molineaux-Thomas' force of infection. The analysis was intended to provide a formal notation that complete the classical equations proposed by these authors.     

Das Rechnen mit Wahrscheinlichkeiten in der Humangenetik

The notation and rules of probability calculus for risk calculations in families and the parameters of Mendelian models are described.     

Matrix notation for efficient development of first-principles models within PAT applications: integrated modeling of antibiotic production with Streptomyces coelicolor

A matrix notation coupled to macroscopic principles is introduced as a means to develop first- principles models in an efficient and structured way within PAT applications. The notation was evaluated for developing an integrated biological, chemical (pH modeling) and physical (gas-liquid exchange) model for describing antibiotic production with Streptomyces coelicolor in batch fermentations. The model provided statistically adequate fits to all the monitored macroscopic biological, chemical and physical data of the process, except the phosphate uptake dynamics. This phosphate discrepancy is hypothesized to result from the internal storage of phosphate as polyphosphate prior to the exponential growth phase. The antibiotic production was associated with the stationary phase and its kinetics was adequately described using a modified Luedeking-Piret equation. Further, the maintenance was best described by employing a combination of Pirt and Herbert models, a result that was supported by a model-based hypothesis testing. Overall the process knowledge currently incorporated in the model is believed to be useful both for process optimization purposes and for further testing of hypotheses aiming at improving the mechanistic understanding of antibiotic production with S. coelicolor. Last but not least, the matrix notation is believed to be a promising supporting tool for efficient development and communication of complex dynamic models within a PAT framework.     

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations

PURPOSE: The PathVisio-Validator plugin aims to simplify the task of producing biological pathway diagrams that follow graphical standardized notations, such as Molecular Interaction Maps or the Systems Biology Graphical Notation. This plugin assists in the creation of pathway diagrams by ensuring correct usage of a notation, and thereby reducing ambiguity when diagrams are shared among biologists. Rulesets, needed in the validation process, can be generated for any graphical notation that a developer desires, using either Schematron or Groovy. The plugin also provides support for filtering validation results, validating on a subset of rules, and distinguishing errors and warnings.     

Some extensions of the use of matrices in population theory

This paper extends Leslie's vector and matrix treatment of populations. A simple matrix is given for species in which adult mortality and fertility are independent of age, but in which the juvenile mortality rate differs from the adult. The population vector can be changed into a population matrix. This should allow equations using functions of the size of the population to be developed. Genetic variables such as sex or other polymorphisms can be introduced, and the notation allows different systems of selection or non-random mating to be specified.