Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes.

Fluorescence in situ hybridization (FISH) is a powerful tool for physical mapping in human and other mammalian species. However, application of the FISH technique has been limited in plant species, especially for mapping single- or low-copy DNA sequences, due to inconsistent signal production in plant chromosome preparations. Here we demonstrate that bacterial artificial chromosome (BAC) clones can be mapped readily on rice (Oryza sativa L.) chromosomes by FISH. Repetitive DNA sequences in BAC clones can be suppressed efficiently by using rice genomic DNA as a competitor in the hybridization mixture. BAC clones as small as 40 kb were successfully mapped. To demonstrate the application of the FISH technique in physical mapping of plant genomes, both anonymous BAC clones and clones closely linked to a rice bacterial blight-resistance locus, Xa21, were chosen for analysis. The physical location of Xa21 and the relationships among the linked clones were established, thus demonstrating the utility of FISH in plant genome analysis.

Hayek and complexity: coordination, evolution and methodology in social adaptive systems

The affinity between the work of the Austrian economist Friedrich A. Hayek and the approach of Complexity Economics is widely recognized by the literature. In spite of this, there still is a lack of studies that seek to analyze in depth the relationship between Hayek and complexity. This dissertation is a contribution to the filling of this large gap in the literature. In the first part of the work, we analyze the various periods in the development of Hayek\'s vision of complexity, showing that this vision is strongly present in his works on knowledge, competition, methodology, evolution, and spontaneous order. In the second part, we explore how Hayek was influenced by two of the main precursors of modern complexity theory - cybernetics and general system theory - from the time he was working on his book on theoretical psychology, The Sensory Order (1952), until the end of his intellectual career.

Theory of strongly correlated electron systems. I. Intersite coulomb interaction and the approximation of renormalized fermions in total energy calculations

The diagrammatic strong-coupling perturbation theory (SCPT) for correlated electron systems is developed for intersite Coulomb interaction and for a nonorthogonal basis set. The construction is based on iterations of exact closed equations for many - electron Green functions (GFs) for Hubbard operators in terms of functional derivatives with respect to external sources. The graphs, which do not contain the contributions from the fluctuations of the local population numbers of the ion states, play a special role: a one-to-one correspondence is found between the subset of such graphs for the many - electron GFs and the complete set of Feynman graphs of weak-coupling perturbation theory (WCPT) for single-electron GFs. This fact is used for formulation of the approximation of renormalized Fermions (ARF) in which the many-electron quasi-particles behave analogously to normal Fermions. Then, by analyzing: (a) Sham's equation, which connects the self-energy and the exchange- correlation potential in density functional theory (DFT); and (b) the Galitskii and Migdal expressions for the total energy, written within WCPT and within ARF SCPT, a way we suggest a method to improve the description of the systems with correlated electrons within the local density approximation (LDA) to DFT. The formulation, in terms of renormalized Fermions LIDA (RF LDA), is obtained by introducing the spectral weights of the many electron GFs into the definitions of the charge density, the overlap matrices, effective mixing and hopping matrix elements, into existing electronic structure codes, whereas the weights themselves have to be found from an additional set of equations. Compared with LDA+U and self-interaction correction (SIC) methods, RF LDA has the advantage of taking into account the transfer of spectral weights, and, when formulated in terms of GFs, also allows for consideration of excitations and nonzero temperature. Going beyond the ARF SCPT, as well as RF LIDA, and taking into account the fluctuations of ion population numbers would require writing completely new codes for ab initio calculations. The application of RF LDA for ab initio band structure calculations for rare earth metals is presented in part 11 of this study (this issue). (c) 2005 Wiley Periodicals, Inc.

Advanced mean field methods:theory and practice

A major problem in modern probabilistic modeling is the huge computational complexity involved in typical calculations with multivariate probability distributions when the number of random variables is large. Because exact computations are infeasible in such cases and Monte Carlo sampling techniques may reach their limits, there is a need for methods that allow for efficient approximate computations. One of the simplest approximations is based on the mean field method, which has a long history in statistical physics. The method is widely used, particularly in the growing field of graphical models. Researchers from disciplines such as statistical physics, computer science, and mathematical statistics are studying ways to improve this and related methods and are exploring novel application areas. Leading approaches include the variational approach, which goes beyond factorizable distributions to achieve systematic improvements; the TAP (Thouless-Anderson-Palmer) approach, which incorporates correlations by including effective reaction terms in the mean field theory; and the more general methods of graphical models. Bringing together ideas and techniques from these diverse disciplines, this book covers the theoretical foundations of advanced mean field methods, explores the relation between the different approaches, examines the quality of the approximation obtained, and demonstrates their application to various areas of probabilistic modeling.

The triune brain in antiquity: Plato, Aristotle, Erasistratus

Tripartite neuropsychologies have featured through two and half millennia of Western thought. They received a modern airing in Paul MacLean's well-known text The Triune Brain. This paper examines the origin of these triune psychophysiologies. It is argued that the first such psychophysiology was developed in the fifth century BCE in the Republic and its Pythagorean sequel, the Timaeus. Aristotle, Plato's pupil and colleague, developed a somewhat similar theory, though this time based on his exhaustive biological researches. Finally, a generation later, Herophilus and Erasistratus at the Alexandrian Museum put together a more anatomically informed tripartite theory that, somewhat modified by Galen in the second century AD, remained the prevailing orthodoxy for nearly fifteen hundred years until it was overturned by the great figures of the Renaissance. Nonetheless, as already mentioned, the notion that human neuropsychology is somehow best thought of as having a tripartite structure has remained remarkably resilient and has reappeared time and again in modern and early modern times. This paper investigates its origins and suggests that it is perhaps now time to move on.

Synchronization processes in nonlinear systems and their relation to cortical oscillatory dynamics

This thesis was focused on theoretical models of synchronization to cortical dynamics as measured by magnetoencephalography (MEG). Dynamical systems theory was used in both identifying relevant variables for brain coordination and also in devising methods for their quantification. We presented a method for studying interactions of linear and chaotic neuronal sources using MEG beamforming techniques. We showed that such sources can be accurately reconstructed in terms of their location, temporal dynamics and possible interactions. Synchronization in low-dimensional nonlinear systems was studied to explore specific correlates of functional integration and segregation. In the case of interacting dissimilar systems, relevant coordination phenomena involved generalized and phase synchronization, which were often intermittent. Spatially-extended systems were then studied. For locally-coupled dissimilar systems, as in the case of cortical columns, clustering behaviour occurred. Synchronized clusters emerged at different frequencies and their boundaries were marked through oscillation death. The macroscopic mean field revealed sharp spectral peaks at the frequencies of the clusters and broader spectral drops at their boundaries. These results question existing models of Event Related Synchronization and Desynchronization. We re-examined the concept of the steady-state evoked response following an AM stimulus. We showed that very little variability in the AM following response could be accounted by system noise. We presented a methodology for detecting local and global nonlinear interactions from MEG data in order to account for residual variability. We found crosshemispheric nonlinear interactions of ongoing cortical rhythms concurrent with the stimulus and interactions of these rhythms with the following AM responses. Finally, we hypothesized that holistic spatial stimuli would be accompanied by the emergence of clusters in primary visual cortex resulting in frequency-specific MEG oscillations. Indeed, we found different frequency distributions in induced gamma oscillations for different spatial stimuli, which was suggestive of temporal coding of these spatial stimuli. Further, we addressed the bursting character of these oscillations, which was suggestive of intermittent nonlinear dynamics. However, we did not observe the characteristic-3/2 power-law scaling in the distribution of interburst intervals. Further, this distribution was only seldom significantly different to the one obtained in surrogate data, where nonlinear structure was destroyed. In conclusion, the work presented in this thesis suggests that advances in dynamical systems theory in conjunction with developments in magnetoencephalography may facilitate a mapping between levels of description int he brain. this may potentially represent a major advancement in neuroscience.

Cognitive systems associated with the hippocampus of the human brain and their role in behaviour and neurodegenerative disease

Cognitive systems research involves the synthesis of ideas from natural and artificial systems in the analysis, understanding, and design of all intelligent systems. This chapter discusses the cognitive systems associated with the hippocampus (HC) of the human brain and their possible role in behaviour and neurodegenerative disease. The hippocampus (HC) is concerned with the analysis of highly abstract data derived from all sensory systems but its specific role remains controversial. Hence, there have been three major theories concerning its function, viz., the memory theory, the spatial theory, and the behavioral inhibition theory. The memory theory has its origin in the surgical destruction of the HC, which results in severe anterograde and partial retrograde amnesia. The spatial theory has its origin in the observation that neurons in the HC of animals show activity related to their location within the environment. By contrast, the behavioral inhibition theory suggests that the HC acts as a ‘comparator’, i.e., it compares current sensory events with expected or predicted events. If a set of expectations continues to be verified then no alteration of behavior occurs. If, however, a ‘mismatch’ is detected then the HC intervenes by initiating appropriate action by active inhibition of current motor programs and initiation of new data gathering. Understanding the cognitive systems of the hippocampus in humans may aid in the design of intelligent systems involved in spatial mapping, memory, and decision making. In addition, this information may lead to a greater understanding of the course of clinical dementia in the various neurodegenerative diseases in which there is significant damage to the HC.

Diagnostic Systems in Medicine as Personal Intellectual Tooling

The standards of diagnostic systems formation in medicine based on modeling expert’s “means of action” in form of illegible trees of solution-making taking into consideration the criteria of credibility and usefulness have been suggested. The fragments of “applied” trees at diagnosing infectious and urological diseases have been considered as well. The possibilities of modern tooling theory usage for decision-making during creation of artificial intelligence systems have been discussed.

Analogical Reasoning Techniques in Intelligent Counterterrorism Systems

The paper develops a set of ideas and techniques supporting analogical reasoning throughout the life-cycle of terrorist acts. Implementation of these ideas and techniques can enhance the intellectual level of computer-based systems for a wide range of personnel dealing with various aspects of the problem of terrorism and its effects. The method combines techniques of structure-sensitive distributed representations in the framework of Associative-Projective Neural Networks, and knowledge obtained through the progress in analogical reasoning, in particular the Structure Mapping Theory. The impact of these analogical reasoning tools on the efforts to minimize the effects of terrorist acts on civilian population is expected by facilitating knowledge acquisition and formation of terrorism-related knowledge bases, as well as supporting the processes of analysis, decision making, and reasoning with those knowledge bases for users at various levels of expertise before, during, and after terrorist acts.

A solution for information management in logistics operations of modern manufacturing chains

One dominant feature of the modern manufacturing chains is the movement of goods. Manufacturing companies would remain an unprofitable investment if the supplies/logistics of raw materials, semi-finished products or final goods are not handled in an effective way. Both levels of a modern manufacturing chain-actual production and logistics-are characterized by continuous data creation at a much faster rate than they can be meaningfully analyzed and acted upon manually. Often, instant and reliable decisions need to be taken based on huge, previously inconceivable amounts of heterogeneous, contradictory or incomplete data. The paper will highlight aspects of information flows related to business process data visibility and observability in modern manufacturing networks. An information management platform developed in the framework of the EU FP7 project ADVANCE will be presented.

Hiánygazdaság − többletgazdaság. Tanulmány a piac elméletéről – II. rész = Shortage economy - surplus economy. A study on market theory II

A főáramlat közgazdászai elismerik, hogy a szocialista rendszert a krónikus hiány jellemezte, de úgy vélik, hogy a kapitalista rendszerben - kisebb vagy nagyobb ingadozások közepette - piaci egyensúly uralkodik. Ezzel szemben a tanulmány két piaci állapotot állít egymással szembe. Az egyikben dominálnak a túlkeresleti jelenségek, bár előfordulnak túlkínálati jelenségek is, ezt nevezi a szerző hiánygazdaságnak. A másikban dominálnak a túlkínálati jelenségek, bár előfordulnak túlkeresleti jelenségek is, amit a szerző többletgazdaságnak nevez. A tanulmány II. része összefoglalja a tanulmány fő állításait. Ezek szerint a szocialista rendszer veleszületett immanens tulajdonsága a hiánygazdaság, míg a kapitalista rendszer veleszületett immanens tulajdonsága a többletgazdaság létrehozása és állandó reprodukciója. Állami beavatkozások erősíthetik vagy gyengíthetik ezeket a genetikus tulajdonságokat, de nem szüntethetik meg. A tanulmány áttekinti a többletgazdaság kedvező és kedvezőtlen hatásait. A kedvező hatások között különleges nyomatékkal emeli ki, hogy a többlet (elsősorban többletkapacitások) nélkül nem alakulhat ki a termelők, illetve az eladók rivalizálása, ami az innovációs folyamat legfontosabb hajtóereje. A többletgazdaság általános esetének vizsgálata után különböző speciális esetekkel foglalkozik a tanulmány: a gazdaság konjunkturális hullámzásával, a hadigazdasággal, a modern kapitalizmusban mutatkozó történelmi léptékű változásokkal, valamint a szocialista rendszeren belül megjelent piacorientált reformokkal és a posztszocialista átmenettel. ____ Mainstream economists recognize that the socialist system was marked by chronic shortage, but they consider that the capitalist system exhibits market equilibrium, give or take some greater or lesser fluctuations. This study, however, contrasts two market states. One is dominated by phenomena of excess demand, though instances of excess supply appear as well; this the author calls a shortage economy. The other is dominated by phenomena of excess supply, though instances of excess demand appear as well; this the author terms a surplus economy. Part II of the study starts by summing up its main propositions. Just as the shortage economy is an intrinsic, immanent trait of the socialist system, so the creation and continual reproduction of the surplus economy is an intrinsic, immanent trait of the capitalist system. Such genetic traits may be strengthened or weakened by state intervention, but not eliminated by it. The study reviews the favourable and detrimental effects of the surplus economy. Of the favourable effects, it is emphasized that without surplus there cannot develop among producers or sellers the rivalry that provides the main impetus for the innovation process. Having examined the general case of the surplus economy, the study turns to various special cases: to the trade-cycle fluctuations of the economy, the war economy, the historic changes appearing in modern capitalism, the market-oriented reforms that appear within the socialist system, and the post-socialist transition.

Looking for Determinants of Ontological Security in the Spain of the Crisis

The concept of ontological security has a remarkable echo in the current sociology to describe emotional status of men of late modernity. However, the concept created by Giddens in the eighties has been little used in empirical research covering various sources of risk or uncertainty. In this paper, a scale for ontological security is proposed. To do this, we start from the results of a research focused on the relationship between risk, uncertainty and vulnerability in the context of the economic crisis in Spain. These results were produced through nine focus groups and a telephone survey with standardized questionnaire applied to a national sample of 2,408 individuals over 18 years. This work is divided into three main sections. In the fi rst, a scale has been built from the results of the application of different items present in the questionnaire used. The second part explores the relationships of the scale obtained with the variables further approximate the emotional dimensions of individuals. The third part observes the variables that contribute to changes in the scale: These variables show the structural feature of the ontological security.

The Collusion of Feminist and Postmodernist Impulses in E.L. Doctorow’s "Ragtime"

Many critics of Doctorow have classified him as a postmodernist writer, acknowledging that a wide number of thematic and stylistic features of his early fiction emanate from the postmodern context in which he took his first steps as a writer. Yet, these novels have an eminently social and ethical scope that may be best perceived in their intellectual engagement and support of feminist concerns. This is certainly the case of Doctorow’s fourth and most successful novel, Ragtime. The purpose of this paper will be two-fold. I will explore Ragtime’s indebtedness to postmodern aesthetics and themes, but also its feminist elements. Thus, on the one hand, I will focus on issues of uncertainty, indeterminacy of meaning, plurality and decentering of subjectivity; on the other hand, I will examine the novel’s attitude towards gender oppression, violence and objectification, its denunciation of hegemonic gender configurations and its voicing of certain feminist demands. This analysis will lead to an examination of the problematic collusion of the mostly white, male, patriarchal aesthetics of postmodernism and feminist politics in the novel. I will attempt to establish how these two traditionally conflicting modes coexist and interact in Ragtime.

The Influence of Limited Kinematic Hardening in Shakedown Analysis

The use of the Design by Analysis concept is a trend in modern pressure vessel and piping calculations. DBA flexibility allow us to deal with unexpected configurations detected at in-service inspections. It is also important, in life extension calculations, when deviations of the original standard hypotesis adopted initially in Design by Formula, can happen. To apply the DBA to structures under variable mechanic and thermal loads, it is necessary that, alternate plasticity and incremental collapse (with instantaneous plastic collapse as a particular case), be precluded. These are two basic failure modes considered by ASME or European Standards in DBA. The shakedown theory is the tool available to achieve this goal. In order to apply it, is necessary only the range of the variable loads and the material properties. Precise, robust and efficient algorithms to solve the very large nonlinear optimization problems generated in numerical applications of the shakedown theory is a recent achievement. Zouain and co-workers developed one of these algorithms for elastic ideally-plastic materials. But, it is necessary to consider more realistic material properties in real practical applications. This paper shows an enhancement of this algorithm to dealing with limited kinematic hardening, a typical property of the usual steels. This is done using internal thermodynamic variables. A discrete algorithm is obtained using a plane stress, mixed finite element, with internal variable. An example, a beam encased in an end, under constant axial force and variable moment is presented to show the importance of considering the limited kinematic hardening in a shakedown analysis.

A recipe for scavenging in vertebrates - the natural history of a behaviour

Despite its prevalence, the importance of scavenging to carnivores is difficult to ascertain in modern day forms and impossible to study directly in extinct species. Yet, there are certain intrinsic and environmental features of a species that push it towards a scavenging lifestyle. These can be thought of as some of the principal parameters in optimal foraging theory namely, encounter rate and handling time. We use these components to highlight the morphologies and environments that would have been conducive to scavenging over geological time by focusing on the dominant vertebrate groups of the land, sea and air. The result is a synthesis on the natural history of scavenging. The features that make up our qualitative scale of scavenging can be applied to any given species and allow us to judge the likely importance of this foraging behaviour.