An algebraic model of an associative noise-like coding memory

A mathematical model of an associative memory is presented, sharing with the optical holography memory systems the properties which establish an analogy with biological memory. This memory system-developed from Gabor's model of memoryis based on a noise-like coding of the information by which it realizes a distributed, damage-tolerant, equipotential storage through simultaneous state changes of discrete substratum elements. Each two associated items being stored are coded by each other by means of two noise-like patterns obtained from them through a randomizing preprocessing. The algebraic braic transformations operating the information storage and retrieval are matrix-vector products involving Toeplitz type matrices. Several noise-like coded memory traces are superimposed on a common substratum without crosstalk interference; moreover, extraneous noise added to these memory traces does not injure the stored information. The main performances shown by this memory model are: i) the selective, complete recovering of stored information from incomplete keys, both mixed with extraneous information and translated from the position learnt; ii) a dynamic recollection where the information just recovered acts as a new key for a sequential retrieval process; iii) context-dependent responses. The hypothesis that the information is stored in the nervous system through a noise-like coding is suggested. The model has been simulated on a digital computer using bidimensional images.     

Sequential configuration model for firing patterns in local neural networks

This paper presents a sequential configuration model to represent the coordinated firing patterns of memory traces in groups of neurons in local networks. Computer simulations are used to study the dynamic properties of memory traces selectively retrieved from networks in which multiple memory traces have been embedded according to the sequential configuration model. Distinct memory traces which utilize the same neurons, but differ only in temporal sequencing are selectively retrievable. Firing patterns of constituent neurons of retrieved memory traces exhibit the main properties of neurons observed in multi microelectrode recordings. The paper shows how to adjust relative synaptic weightings so as to control the disruptive influences of cross-talk in multipy-embedded networks. The theoretical distinction between (primarily anatomical) beds and (primarily physiological) realizations underlines the fundamentally stochastic nature of network firing patterns, and allows the definition of 4 degrees of clarity of retrieved memory traces.     

A working memory model for serial order that stores information in the intrinsic excitability properties of neurons

Models for temporary information storage in neuronal populations are dominated by mechanisms directly dependent on synaptic plasticity. There are nevertheless other mechanisms available that are well suited for creating short-term memories. Here we present a model for working memory which relies on the modulation of the intrinsic excitability properties of neurons, instead of synaptic plasticity, to retain novel information for periods of seconds to minutes. We show that it is possible to effectively use this mechanism to store the serial order in a sequence of patterns of activity. For this we introduce a functional class of neurons, named gate interneurons, which can store information in their membrane dynamics and can literally act as gates routing the flow of activations in the principal neurons population. The presented model exhibits properties which are in close agreement with experimental results in working memory. Namely, the recall process plays an important role in stabilizing and prolonging the memory trace. This means that the stored information is correctly maintained as long as it is being used. Moreover, the working memory model is adequate for storing completely new information, in time windows compatible with the notion of “one-shot” learning (hundreds of milliseconds).     

mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics

Background  

Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other relevant data, e.g. formulas, chemical structures, identification numbers to other databases etc. Since existing solutions are either commercial and therefore only available for certain instruments or not capable of storing such information, there is need to provide a software tool for the management of such data.     

Trace feature map: a model of episodic associative memory

An approach to episodic associative memory is presented, which has several desirable properties as a human memory model. The design is based on topological feature map representation of data. An ordinary feature map is a classifier, mapping an input vector onto a topologically meaningful location on the map. A trace feature map, in addition, creates a memory trace on that location. The traces can be stored episodically in a single presentation, and retrieved with a partial cue. Nearby traces overlap, which results in plausible memory interference behavior. Performance degrades gracefully as the memory is overloaded. More recent traces are easier to recall as are traces that are unique in the memory.This research was supported in part by an ITA Foundation grant and by fellowships from the Academy of Finland, the Emil Aaltonen Foundation and the Foundation for the Advancement of Technology (Finland) when the author was at UCLA     

Modelling memory functions with recurrent neural networks consisting of input compensation units: II. Dynamic situations

Modelling the cognitive abilities of humans or animals or building agents that are supposed to behave cognitively requires modelling a memory system that is able to store and retrieve various contents. The content to be stored is assumed to comprise information about more or less invariant environmental objects as well as information about movements. A combination of information about both objects and movements may be called a situation model. Here we focus, in part, on models storing dynamic patterns. In particular, two abilities of humans in representing dynamical systems receive special focus: the capability of representing the acceleration of objects, as can be found in the movement of a pendulum or freely falling objects, and the capability of representing actions of transfer, i.e. motion from one point to another, have been modelled using recurrent networks consisting of input compensation units. In addition, possibilities of combining static and dynamic properties within a single model are studied.     

An after-shannon measure of the storage capacity of an associative noise-like coding memory

The maximum amount of information that can be stored, on the average, in each storage element, according to an associative scheme, has been measured for the memory model proposed by the author (Bottini 1980). In this model, the (binary) items being stored are coded by noise-like keys and the memory traces formed in this way are superimposed, by algebraic addition, on the same many-level storage elements. It is shown that the problem of measuring the information retrieved from the memory in a single recall and the problem — concerning the data-communication field —of measuring the information transmitted over a noisy channel are formally similar. In particular, the Shannon noisy-channel coding theorem can find an application also in our case of an associative memory. Finally, it is evidenced that the so-called matrix model of an associative memory has the same storage capacity as the model studied here.     

Seasonal Mortality Patterns in Primates: Implications for the Interpretation of Dental Microwear

The microscopic traces of use wear on teeth have been extensively studied to provide information that will assist in elucidating the dietary habits of extinct hominin species. 1 - 13 It has been amply documented that dental microwear provides information pertaining to diet for living animals, where there is a strong and consistent association between dental microwear patterns and different types of foods that are chewed. The details of occlusal surface wear patterns are capable of distinguishing among diets when the constituent food items differ in their fracture properties. 14 - 20 For example, the microwear traces left on the teeth of mammals that crush hard, brittle foods such as nuts are generally dominated by pits, whereas traces left on the teeth of mammals that shear tough items such as leaves tend to be characterized by scratches. These microwear features result from and thus record actual chewing events. As such, microwear patterns are expected to be variably ephemeral, as individual features are worn away and replaced or overprinted by others as the tooth wears down in subsequent bouts of mastication. Indeed, it has been demonstrated, both in the laboratory and the wild, that short‐term dietary variation can result in the turnover of microwear. 17 , 21 - 23 Because occlusal microwear potentially reflects an individual's diet for a short time (days, weeks, or months, depending on the nature of the foods being masticated), tooth surfaces sampled at different times will display differences that relate to temporal (for example, seasonal) differences in diet. 24     

Synthetic polymers and their potential as genetic materials

DNA and RNA are the only known natural genetic materials. Systematic modification of each of their chemical building blocks (nucleobase, sugar, and phosphate) has enabled the study of the key properties that make those nucleic acids genetic materials. All three moieties contribute to replication and, significantly, all three moieties can be replaced by synthetic analogs without loss of function. Synthetic nucleic acid polymers capable of storing and propagating information not only expand the central dogma, but also highlight that DNA and RNA are not unique chemical solutions for genetic information storage. By considering replication as a question of information transfer, we propose that any polymer that can be replicated could serve as a genetic material. Editor's suggested further reading in BioEssays Xenobiology: A new form of life as the ultimate biosafety tool Abstract     

A Model of the Hippocampal–cortical Memory System

Based on physiological evidence, we propose a theoretical model of the hippocampal–cortical memory system. The model consists of the following components: the sensory system, the hippocampus (short-term memory), and the association cortex (long-term memory). A series of key codes (local information) is supplied from the sensory system, while context (global information) is inputted from the hippocampus. The two inputs interact dynamically in the association cortex. The interactive neurons work as a detector of coincidence. The cortical network learns the memory information through the coincidence window and, finally, stores it in the form of attractors. This local–global information works as an addressor to designate the stored location of the memory in the association cortex and accelerates the process of storing and retrieving memory information.     

蛋白质：生物界中又一类信息的储存者和传递者 ——对 prion 生物学相关知识的重新解读

蛋白质在相当一段时间内一直被认为只是 DNA 或 RNA 等遗传物质的表达形式,其单独不具有储存和传递生物信息的功能,而储存和传递生物信息却是遗传物质的两个基本属性 . 随着近年来 prion 生物学的出现和研究的逐步深入,人们已经认识到蛋白质单独就具有储存和传递生物信息的功能,从这个意义上讲,蛋白质也是一类遗传物质 . 所以很有必要站在这个角度对 prion 生物学的相关知识进行重新的梳理和再认识,通过对哺乳动物 prion 生物学和真菌 prion 生物学各自发展历程的简要回顾和最新研究成果的介绍,以及它们之间相同点和不同点的比较,总结出蛋白质储存和传递生物信息的一般规律并指出其表现形式的多样性 .     

Some theoretical aspects of reprogramming the standard genetic code

Reprogramming of the standard genetic code to include non-canonical amino acids (ncAAs) opens new prospects for medicine, industry, and biotechnology. There are several methods of code engineering, which allow us for storing new genetic information in DNA sequences and producing proteins with new properties. Here, we provided a theoretical background for the optimal genetic code expansion, which may find application in the experimental design of the genetic code. We assumed that the expanded genetic code includes both canonical and non-canonical information stored in 64 classical codons. What is more, the new coding system is robust to point mutations and minimizes the possibility of reversion from the new to old information. In order to find such codes, we applied graph theory to analyze the properties of optimal codon sets. We presented the formal procedure in finding the optimal codes with various number of vacant codons that could be assigned to new amino acids. Finally, we discussed the optimal number of the newly incorporated ncAAs and also the optimal size of codon groups that can be assigned to ncAAs.     

Thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3

The characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. NMR has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. In this article we show that it is also possible to discriminate the kinetic properties of individual centres in multihaem proteins, if the complete microscopic thermodynamic characterisation is available and the system displays fast intramolecular equilibration in the time scale of the kinetic experiment. The deconvolution of the kinetic traces using a model of thermodynamic control provides a reference rate constant for each haem that does not depend on driving force and can be related to structural factors. The thermodynamic characterisation of three tetrahaem cytochromes and their kinetics of reduction by sodium dithionite are reported in this paper. Thermodynamic and kinetic data were fitted simultaneously to a model to obtain microscopic reduction potentials, haem-haem and haem-proton interacting potentials, and reference rate constants for the haems. The kinetic information obtained for these cytochromes and recently published data for other multihaem cytochromes is discussed with respect to the structural factors that determine the reference rates. The accessibility for the reducing agent seems to play an important role in controlling the kinetic rates, although is clearly not the only factor.     

Why some tits store food and others do not: evaluation of ecological factors

Paridae are among the bird families benefiting from food storing. However, not all its members hoard food. Our objective was to clarify the role of ecological factors in occurrence of food storing. We reviewed the data on major ecological characteristics of the Paridae species and analysed their association with the presence/absence of food storing. Our statistical model revealed that geography (distribution in North America) and taxonomy (genus Poecile) are better predictors of food storing than any of the studied ecological traits. Nevertheless, food-storing Poecile species inhabit mixed or coniferous woodlands with seasonal richness of food, while non-storing species tend to prefer edge and open habitats, where alternative food sources are available. Sociality and territoriality outside breeding season coincides with food storing. The analysis performed within the Baeolophus–Lophophanes–Periparus–Poecile clade with ancestral food storing revealed no factor except continental climate that would explain the persistence of food storing. The phylogenetic analysis of ancestral states of the studied characters allowed us to propose a possible scenario for the emergence of food storing in Paridae. (1) Food storing is not ancestral in Paridae and appeared only once in the common ancestor of the Baeolophus–Lophophanes–Periparus–Poecile group. (2) According to estimation of molecular clock in Paridae, food storing appeared before their radiation in North America.     

Exploring the Mechanism of General Anesthesia: Kinetic Analysis of GABAA Receptor Electrophysiology

A kinetic model of the effect of agonist and anesthetics on ligand-gated ion channels, developed in earlier work, is further refined and used to predict traces observed in fast-perfusion electrophysiological studies on recombinant GABA_A receptors under a wide range of agonist and/or anesthetic concentrations. The model incorporates only three conformational states (resting, open, and desensitized) but allows for the modulation of the conformational free energy landscape connecting these states resulting from adsorption of agonist and/or anesthetic to the bilayer in which the protein is embedded. The model is shown to reproduce the diverse and complex features of experimental traces remarkably well, including both anesthetic-induced and agonist-induced traces, as well as the modulation of agonist-induced traces by anesthetic, either coapplied or continuously present. The solutions to the kinetic equations, which give the time-dependence of each of the nine protein states (three ligation states for each of the three conformations), describe the flow of probability among these states and thus reveal the kinetic underpinnings of the traces. Many of the parameters in the model, such as the desorption rate constants of anesthetic and agonist, are directly related to model-independent experimental measurements and thus can serve as a definitive test of its validity.     

A first global analysis of plasmid encoded proteins in the ACLAME database

Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entities, their genomes display a mosaic and combinatorial structure, making their classification extremely difficult. As other MGEs, plasmids play a major role in horizontal transfer of genetic materials and genome reorganization. Yet, the full impact of such phenomenon on major properties of the host cell, such as pathogenicity, the ability to use new carbon sources or resistance to antibiotics, remains to be fully assessed. More and more complete plasmid genome sequences are available. However, in the absence of standards for storing plasmid sequence data and annotating genes and gene products on sequenced plasmid genomes, the resulting information remains rather limited. Using 503 sequenced plasmids organized in the ACLAME database, we discuss how, by structuring information on the genomes, their host and the proteins they code for, one can gain access to either global or more detailed analysis of the plasmid sequence information, as illustrated by a network representation of the relationships between plasmids.     

A Suite of Dermestid Beetle Traces on Dinosaur Bone from the Upper Jurassic Morrison Formation,Wyoming, USA

Most studies of insect traces on fossil bone deal with one or two trace morphs found on isolated bone fragments, making it difficult to identify the trace-maker and its behavior. We report the discovery of a suite of insect traces on an articulated Camptosaurus dinosaur skeleton that permits the identification of the trace-maker and interpretations of its behavior. The traces include mandible marks, pits, and shallow bores on cortical bone, and deep, meandering furrows and tunnels (borings) on articular surfaces. The interiors of bones are intensely mined, and the cavities and borings are filled with fine bone fragments (insect frass). The distinctive mandible marks consist of opposing sets of parallel grooves, indicating the maker had two apical teeth set on symmetrical mandibles and that all of the traces were made by a single taxon. Comparison of the fossils with the mandible morphology and bone traces of extant insects indicates dermestid beetles made the traces. Based on extant dermestid behavior, soft tissues were likely absent and the bones were lipid-laden when the traces were made. Examination of more than 5,000 bones from the Morrison and Cedar Mountain formations shows insect traces on bone are common but overlooked and that many bones are substantially damaged by insect mining. The key to the recognition of these important yet subtle traces is a search model and an intense, oblique light source.     

Stereographic reconstruction of human brain CT series

A relatively simple method for the three-dimensional reconstruction of brain contours from a series of CT scans is presented. A procedure is described for storing the structural information obtained from the CT series and for organizing and displaying the data. Furthermore, it is shown how additional features such as standardized artery information taken from an atlas can be superimposed on the spatially reconstructed brain model. It is proposed that three-dimensional representations in the form of computed stereo pairs are quite suitable for morphological documentation of specific neuropsychological issues, such as the localization of aphasic syndromes.