Voice-printing of the Nightjar, Caprimulgus europaeus

The usual way of analysing bird-song is by use of a conagraph, which produces a plot of frequency as a function of time, for perods of up to about 2.5 s. This method is fully described by Catchpole (1979), Jellis (1977) and Thorpe (1961). In the present work, a Brüel and Kjaer Narrow Band Spectrum Analyser was used to analyse up to two minutes of bird-song. This instrument produces a fast Fourier analysis of the input in the form of a spectrum of sound pressure level against frequency. Studies of seven Nightjars. Caprimulgus europaeus . show that each individual produces its own characteristic voice spectrum enabling individual birds to be identified with much greater ease than from a sonagram.     

A graphical notation for biochemical networks

A solid definition and comprehensive graphical representation of biological networks is essential for efficient and accurate dissemination of information on biological models. Several proposals have already been made toward this aim. The most well known representation of this kind is a molecular interaction map, or ‘Kohn Map’. However, although the molecular interaction map is a well-defined and compact notation, there are several drawbacks, such as difficulties in intuitive understanding of temporal changes of reactions and additional complexities arising from particular graphical representations. This article proposes several improvements to the molecular interaction map, as well as the use of the ‘process diagram’ to help understand temporal sequences of reactions.     

鸣禽发声学习记忆与即刻早期基因

鸣禽受到声音信号的刺激或自身表现出发声行为时,脑内即刻早期基因(immediate early gene,IEG)能迅速被激活而表达.其中zenk、c-fos和c-jun表达的脑区及水平与鸟在鸣唱时神经元的活动区域及活动程度相一致,暗示IEG在鸣禽发声学习记忆中起重要作用.     

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 Simple Method for Handling Grids

A simple method for handling electron microscope grids is described here. While assuring their identification and safety, this method provides improved handling, temporary storage, and identification of grids bearing ultra-thin sections, and in addition, provides a novel method for preparing bulk samples. Grids are attached at their edges to the weakly adhesive surface of a “Post-it” note pad which sits in a petri dish. The grids are safely immobilized on the pad, classified based on their location, and identified by convenient pad notation. Grid manipulation and identification are simplified using this device, which is easily assembled from readily available and inexpensive materials.     

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.     

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.     

A proposal for a convenient notation for P-chiral nucleotide analogues. Part 2. Dinucleoside monophosphate analogues

A configuration of ligands around a phosphorus atom in P-chiral dinucleoside monophosphate analogues can be described using DP/LP stereochemical notation, which allows immediate correlation between the notation of configuration and the actual spatial arrangement of the phosphorus ligands. The area of applications of this new stereochemical nomenclature covers dinucleoside units bridged by virtually any type of tri-and tetra-coordinated phosphorus moieties, that is, phosphorothioates, phosphoramidates, phosphoramidites, boranephosphates, methanephosphonates, H-phosphonates, and many others.     

A proposal for a convenient notation for P-chiral nucleotide analogues. Part 2. Dinucleoside monophosphate analogues

A configuration of ligands around a phosphorus atom in P-chiral dinucleoside monophosphate analogues can be described using D_P/L_P stereochemical notation, which allows immediate correlation between the notation of configuration and the actual spatial arrangement of the phosphorus ligands. The area of applications of this new stereochemical nomenclature covers dinucleoside units bridged by virtually any type of tri-and tetra-coordinated phosphorus moieties, that is, phosphorothioates, phosphoramidates, phosphoramidites, boranephosphates, methanephosphonates, H-phosphonates, and many others.     

The perception of music.

A common but none the less remarkable human faculty is the ability to recognize and reproduce familiar pieces of music. No two performances of a given piece will ever be acoustically identical, but a listener can perceive, in both, the same rhythmic and tonal relationships, and can judge whether a particular note or phrase was played out of time or out of tune. The problem considered in this lecture is that of describing the conceptual structures by which we represent Western classical music and the processes by which these structures are created. Some new hypotheses about the perception of rhythm and tonality have been cast in the form of a computer program which will transcribe a live keyboard performance of a classical melody into the equivalent of standard musical notation.     

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.     

Molecular interaction map of the p53 and Mdm2 logic elements, which control the Off-On switch of p53 in response to DNA damage

The molecular network that controls responses to genotoxic stress is centered at p53 and Mdm2. Recent findings have shown this network to be more complex than previously envisioned. Using a notation specifically designed for circuit diagram-like representations of bioregulatory networks, we have prepared an updated molecular interaction map of the immediate connections of p53 and Mdm2, which are described as logic elements of the network. We use the map as the basis for a comprehensive review of current concepts of signal processing by these logic elements (an interactive version of the maps-eMIMs can be examined at ). We also used molecular interaction maps to propose a p53 Off-On switch in response to DNA damage.