Using sensory weighting to model the influence of canal,otolith and visual cues on spatial orientation and eye movements

 The sensory weighting model is a general model of sensory integration that consists of three processing layers. First, each sensor provides the central nervous system (CNS) with information regarding a specific physical variable. Due to sensor dynamics, this measure is only reliable for the frequency range over which the sensor is accurate. Therefore, we hypothesize that the CNS improves on the reliability of the individual sensor outside this frequency range by using information from other sensors, a process referred to as “frequency completion.” Frequency completion uses internal models of sensory dynamics. This “improved” sensory signal is designated as the “sensory estimate” of the physical variable. Second, before being combined, information with different physical meanings is first transformed into a common representation; sensory estimates are converted to intermediate estimates. This conversion uses internal models of body dynamics and physical relationships. Third, several sensory systems may provide information about the same physical variable (e.g., semicircular canals and vision both measure self-rotation). Therefore, we hypothesize that the “central estimate” of a physical variable is computed as a weighted sum of all available intermediate estimates of this physical variable, a process referred to as “multicue weighted averaging.” The resulting central estimate is fed back to the first two layers. The sensory weighting model is applied to three-dimensional (3D) visual–vestibular interactions and their associated eye movements and perceptual responses. The model inputs are 3D angular and translational stimuli. The sensory inputs are the 3D sensory signals coming from the semicircular canals, otolith organs, and the visual system. The angular and translational components of visual movement are assumed to be available as separate stimuli measured by the visual system using retinal slip and image deformation. In addition, both tonic (“regular”) and phasic (“irregular”) otolithic afferents are implemented. Whereas neither tonic nor phasic otolithic afferents distinguish gravity from linear acceleration, the model uses tonic afferents to estimate gravity and phasic afferents to estimate linear acceleration. The model outputs are the internal estimates of physical motion variables and 3D slow-phase eye movements. The model also includes a smooth pursuit module. The model matches eye responses and perceptual effects measured during various motion paradigms in darkness (e.g., centered and eccentric yaw rotation about an earth-vertical axis, yaw rotation about an earth-horizontal axis) and with visual cues (e.g., stabilized visual stimulation or optokinetic stimulation). Received: 20 September 2000 / Accepted in revised form: 28 September 2001     

Protention and retention in biological systems

This article proposes an abstract mathematical frame for describing some features of cognitive and biological time. We focus here on the so called “extended present” as a result of protentional and retentional activities (memory and anticipation). Memory, as retention, is treated in some physical theories (relaxation phenomena, which will inspire our approach), while protention (or anticipation) seems outside the scope of physics. We then suggest a simple functional representation of biological protention. This allows us to introduce the abstract notion of “biological inertia”.     

On the role of synchrony for neuron–astrocyte interactions and perceptual conscious processing

Recent research on brain correlates of cognitive processes revealed the occurrence of global synchronization during conscious processing of sensory stimuli. In spite of technological progress in brain imaging, an explanation of the computational role of synchrony is still a highly controversial issue. In this study, we depart from an analysis of the usage of blood-oxygen-level-dependent functional magnetic resonance imaging for the study of cognitive processing, leading to the identification of evoked local field potentials as the vehicle for sensory patterns that compose conscious episodes. Assuming the “astrocentric hypothesis” formulated by James M. Robertson (astrocytes being the final stage of conscious processing), we propose that the role of global synchrony in perceptual conscious processing is to induce the transfer of information patterns embodied in local field potentials to astrocytic calcium waves, further suggesting that these waves are responsible for the “binding” of spatially distributed patterns into unitary conscious episodes.     

Terahertz vibrational properties of water nanoclusters relevant to biology

Water nanoclusters are shown from first-principles calculations to possess unique terahertz-frequency vibrational modes in the 1–6 THz range, corresponding to O–O–O “bending,” “squashing,” and “twisting” “surface” distortions of the clusters. The cluster molecular-orbital LUMOs are huge Rydberg-like “S,” “P,” “D,” and “F” orbitals that accept an extra electron via optical excitation, ionization, or electron donation from interacting biomolecules. Dynamic Jahn–Teller coupling of these “hydrated-electron” orbitals to the THz vibrations promotes such water clusters as vibronically active “structured water” essential to biomolecular function such as protein folding. In biological microtubules, confined water-cluster THz vibrations may induce their “quantum coherence” communicated by Jahn–Teller phonons via coupling of the THz electromagnetic field to the water clusters’ large electric dipole moments.     

Image analysis as a tool for quantitative phycology: a computational approach to cyanobacterial taxa identification

In the following work we discuss the application of image processing and pattern recognition to the field of quantitative phycology. We overview the area of image processing and review previously published literature pertaining to the image analysis of phycological images and, in particular, cyanobacterial image processing. We then discuss the main operations used to process images and quantify data contained within them. To demonstrate the utility of image processing to cyanobacteria classification, we present details of an image analysis system for automatically detecting and classifying several cyanobacterial taxa of Lake Biwa, Japan. Specifically, we initially target the genus Microcystis for detection and classification from among several species of Anabaena. We subsequently extend the system to classify a total of six cyanobacteria species. High-resolution microscope images containing a mix of the above species and other nontargeted objects are analyzed, and any detected objects are removed from the image for further analysis. Following image enhancement, we measure object properties and compare them to a previously compiled database of species characteristics. Classification of an object as belonging to a particular class membership (e.g., “Microcystis,”“A. smithii,”“Other,” etc.) is performed using parametric statistical methods. Leave-one-out classification results suggest a system error rate of approximately 3%. Received: September 6, 1999 / Accepted: February 6, 2000     

Gender Victims and Cultural Borders: The Globalization of Prostitution in Italy

In this article I will try to analyse the transformation regarding the italian regulation of prostitution on the grounds of another issue, that is the building up of cultural borders for the definition of “national” and “european” gender identities. The creation of cultural borders allows to outline the differentiation traits between social groups, while escaping plurality and internal contradictions which on the other hand could only show continuity and vicinity traits. In my point of view, the italian current debate on prostitution is a discoursive process that produces a “western” pattern of relation between men and women, while referring internal tensions and contradictions to other cultures. The following analysis will use data and information coming from national official statistics on immigration, estimates on prostitutions and findings from national researchers on prostitution carried out by the research group called “Migration & Prostitutions” based at the Department of Sociology of the Padua University.     

Biosemiosis and the Cellular Basis of Mind

The human brain is a complex organ made up of neurons and several other cell types, and whose role is processing information for use in elicitation of behaviors. To accomplish this, the brain requires large amounts of energy, and this energy is obtained by the oxidation of glucose (Glc). However, the question of how the oxidation of Glc by individual neurons in brain results in their collective ability to rapidly generate feats of cognition that allow them to recognize the nature of the universe in which they live and to communicate this information remains unclear. In this article, insights into this process are provided by first considering the brain’ s homeostatic “operating system” for supply of energy to stimulated neurons, and how this system defines the basic unit of brain “structure”. This is followed by consideration of the brain’s “two-cell” neuronal communication mechanism which defines the basic unit of brain “function”. Finally, an analysis of the nature of frequency-encoded “neuronal languages” that enable ensembles of neurons to translate energy derived from the oxidation of Glc into a collective “mind”, the aggregate of all brain processes including those involving perception, thought, insight, foresight, imagination and behavior.     

A “lookup table” schema for synthetic biological patterning

A schema is proposed by which the three-dimensional structure and temporal development of a biological organism might be encoded and implemented via a genetic “lookup table”. In the schema, diffusive morphogen gradients and/or the global concentration of a quickly diffusing signal index sets of kinase genes having promoters with logarithmically diminished affinity for the signal. Specificity of indexing is enhanced via concomitant expression of phosphatases undoing phosphorylation by “neighboring” kinases of greater affinity. Combinations of thus-selected kinases in turn jointly activate, via multiple phosphorylation, a particular enzyme from a virtual, multi-dimensional array thereof, at locations and times specified within the “lookup table”. In principle, such a scheme could be employed to specify arbitrary gross anatomy, surface pigmentation, and/or developmental sequencing, extending the burgeoning toolset of the nascent field of synthetic morphology. A model of two-dimensional surface coloration using this scheme is specified, and LabVIEW software for its exploration is described and made available.     

“L” forms ofStaphylococcus

Conclusions From the morphological study on the transformation of staphylococci into the “L” phase, we are inclined to conclude that intermediary stages between the coccus and the “L” organisms do not exist. Moreover, our results suggest that possibly two different cells take part in the transformation. In spite of two hundred and more passages in the “L” phase, we have not yet succeeded in obtaining stable “L” forms of staphylococci.

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Résumé Une étude morphologique de la transformation des staphylocoques en phase “L” moyennant un appareil cinématographique nous a suggéré que des stades intermédiaires entre le coccus et les organismes “L” n'existent pas. Nos résultats nous ont fait considérer la possibilité, que dans la transformation deux cellules bactériennes différentes jouent un r?le. Malgré que nous avons fait plus de 200 passages en phase “L” nous n'avons pas réussi à obtenir des colonies “L” stables des staphylocoques.

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Part I: Antonie van Leeuwenhoek 25, 325, 1959.

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Working with grants of the foundation “Prof. Dr. D. A. de Jong-Stichting” and the “Stichting ter Bevordering van Medisch-Wetenschappelijk Onderzoek”.     

Sexes,species, and genomes: why males and females are not like humans and chimpanzees

This paper describes, analyzes, and critiques the construction of separate “male” and “female” genomes in current human genome research. Comparative genomic work on human sex differences conceives of the sexes as like different species, with different genomes. I argue that this construct is empirically unsound, distortive to research, and ethically questionable. I propose a conceptual model of biological sex that clarifies the distinction between species and sexes as genetic classes. The dynamic interdependence of the sexes makes them “dyadic kinds” that are not like species, which are “individual kinds.” The concept of sex as a “dyadic kind” may be fruitful as a remedy to the tendency to conceive of the sexes as distinct, binary classes in biological research on sex more generally.     

In situ feeding tactics of short-nosed fruit bat (Cynopterus sphinx) on mango fruits: evidence of extractive foraging in a flying mammal

We report a sequence of behaviors exhibited by the short-nosed fruit bat Cynopterus sphinx while feeding on fruits of Mangifera indica. They peel off the outer skin to form a feeding area of about 3–6 cm diameter. Such food preparatory behaviors were more pronounced on larger mangoes. Bats competed among themselves to feed on the mangoes that had such feeding areas exposed. Individuals that spent a considerable amount of time on food preparatory behaviors actively secured the fruits. Altogether, these behaviors indicate that Cynopterus bats might have learnt, over evolutionary time, and developed behaviors that facilitate efficient processing and feeding of fruits such as mangoes. It appears that actions exhibited by C. sphinx in peeling off the outer skin of mangoes exemplify “extractive foraging”, a behavior that is prominently known in large-brained mammals. Thus, our findings will have implications on the distribution and evolution of extractive foraging and “technical intelligence” among mammalian lineages.     

Regulatory considerations when developing biological products

The Center for Biologics Evaluation and Research, whose regulatory authority includes monoclonal antibodies, cytokines, vaccines, toxins and somatic cellular therapies, communicates to sponsors issues for consideration in the development of biological products through the publication of “Points to Consider” and “Guideline” documents. This paper summarizes the available “Points to Consider” and “Guideline” documents and outlines recommendations from these documents for characterizing the cells used to produce biological products.     

The Poetics of Purpose

Hackles have been raised in biosemiotic circles by T. L. Short’s assertion that semiosis, as defined by Peirce, entails “acting for purposes” and therefore is not found below the level of the organism (2007a:174–177). This paper examines Short’s teleology and theory of purposeful behavior and offers a remedy to the disagreement. Remediation becomes possible when the issue is reframed in the terms of the complexity sciences, which allows intentionality to be understood as the interplay between local and global aspects of a system within a system. What is called “acting for purposes” is not itself a type of behavior so much as a relationship between a dynamic system that “exists for a purpose” and its microprocesses that “serve purposes.” The “intentional object” of philosophy is recast here as the holistic self-organized dynamics of a system, which exists for the purpose of self-maintenance, and that constrains the parts’ behaviors, which serve the purpose of forming the system. (A “system” can be any emergent, e.g. an abiotic form, an adapted species, a self, a conditioned response, thought, or a set of ideas.) The self-organized whole, which is represented to the parts in their own constrained behaviors, assumes the guiding function so long attributed to the mysterious “intentional object.” If emergent self-causation is not disallowed, creative originality, as well as directionality, becomes part of the definition of purposeful behavior. Thus, key tools used here, required for understanding emergence, come from poetics rather than semoitics. In the microprocesses of self-organization, I find what I call “accidental” indices and icons — which are poetic in the sense that they involve mere metonymic contiguity and metaphoric similarity — and which are preferentially selected under constrained conditions allowing radically new connections to habituate into an “intentional” self-organized system that, not coincidentally, has some of the emergent characteristics of a conventional symbolic system.

Chain processes and their biophysical applications: Part I. General theory

A mathematical theory applicable to the biological effects of radiations as chain processes is developed. The theory may be interpreted substantially as a “hit theory” involving the concepts of “sensitive volume” or “target area”. The variability of the sensitivity of the organism to the radiation and its capacity of recovery between single hits is taken into account. It is shown that in a continuous irradiation of a biological aggregate in which the effect of each single hit cannot be observed, recovery and variation of sensitivity are formally equivalent to each other so that a discrimination between these two phenomena is possible only by discontinuous irradiation or by using different radiation intensities. Methods for the calculation of the “number of hits” and for the determination of the kinetics of the processes from “survival curves” or similar experimental data are given. The relation between the recovery and the Bunsen-Roscoe law is discussed. The case in which the injury of the organism is dependent on the destruction of more than one “sensitive volume” is also considered.     

Life and death near a windy oasis

We propose a simple experiment to study delocalization and extinction in inhomogeneous biological systems. The nonlinear steady state for, say, a bacteria colony living on and near a patch of nutrient or favorable illumination (“oasis”) in the presence of a drift term (“wind”) is computed. The bacteria, described by a simple generalization of the Fisher equation, diffuse, divide A→A + A, die A→ 0, and annihilate A + A→ 0. At high wind velocities all bacteria are blown into an unfavorable region (“desert”), and the colony dies out. At low velocity a steady state concentration survives near the oasis. In between these two regimes there is a critical velocity at which bacteria first survive. If the “desert” supports a small nonzero population, this extinction transition is replaced by a delocalization transition with increasing velocity. Predictions for the behavior as a function of wind velocity are made for one and two dimensions. Received: 3 August 1998 / Revised version: 17 July 1999 / Published online: 4 July 2000     

Detection of gene flow from GM to non-GM watermelon in a field trial

Gene flow from genetically modified (GM) crops to conventional non-GM crops is a serious concern for protection of conventional and organic farming. Gene flow from GM watermelon developed for rootstock use, containing cucumber green mottle mosaic virus (CGMMV)-coat protein (CP) gene, to a non-GM isogenic control variety “Clhalteok” and grafted watermelon “Keumcheon” was investigated in a small scale field trial as a pilot study. Hybrids between GM and non-GM watermelons were screened from 1304 “Chalteok” seeds and 856 “Keumcheon” seeds using the duplex PCR method targeting theCGMMV- CP gene as a marker. Hybrids were found in all pollen recipient plots. The gene flow frequencies were greater for “Chaiteok” than for “KeumcheonD; with 75% outcrossing in the “Chaiteok” plot at the closest distance (0.8 m) to the GM plot. A much larger scale field trial is necessary to identify the isolation distance between GM and non-GM watermelon, as the behaviors of insect pollinators needs to be clarified in Korea.     

Motor pattern selection by combinatorial code of interneuronal pathways

We use a modeling approach to examine ideas derived from physiological network analyses, pertaining to the switch of a motor control network between two opposite control modes. We studied the femur–tibia joint control system of the insect leg, and its switch between resistance reflex in posture control and “active reaction” in walking, both elicited by the same sensory input. The femur–tibia network was modeled by fitting the responses of model neurons to those obtained in animals. The strengths of 16 interneuronal pathways that integrate sensory input were then assigned three different values and varied independently, generating a database of more than 43 million network variants. We demonstrate that the same neural network can produce the two different behaviors, depending on the combinatorial code of interneuronal pathways. That is, a switch between behaviors, such as standing to walking, can be brought about by altering the strengths of selected sensory integration pathways. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

How do bees learn and recognize visual patterns?

The basic task of perceptual systems is the recognition and localization of objects. The central nervous system has to solve these problems on the basis of the excitation patterns of sensory nerves, in spite of the fact that these provide only ambiguous information about objects. Two processing principles seem to be fundamental for an efficient formation of object representations: the extraction of characteristic features and the ability to assess similarities between different objects. This article reviews investigations in which different training paradigms were applied in order to explore the honeybee's capacities to learn and recognize visual patterns. One aim of these experiments is to assess whether insects use similar processing mechanisms as vertebrates, for instance human beings. By comparing the computational performance of perceptual systems in animals with different evolutionary history we can hope to learn more about the operation of basic rules in nervous systems. “The messages which the brain receives have not the least similarity with the stimuli. They consist in pulses of given intensities and frequencies, characteristic for the transmitting nerve-fiber, which ends at a definite place of the cortex. ... From this information it produces the image of the world by a process which can metaphorically be called a consummate piece of combinatorial mathematics: it sorts out of the maze of indifferent and varying signals, invariant shapes and relations which form the world of ordinary experience.” Max Born (1949) Received: 4 October 1997 / Accepted in revised form: 26 August 1998     

Macroevolution via secondary endosymbiosis: a Neo-Goldschmidtian view of unicellular hopeful monsters and Darwin’s primordial intermediate form

Seventy-five years ago, the geneticist Richard Goldschmidt hypothesized that single mutations affecting development could result in major phenotypic changes in a single generation to produce unique organisms within animal populations that he called “hopeful monsters”. Three decades ago, Sarah P. Gibbs proposed that photosynthetic unicellular micro-organisms like euglenoids and dinoflagellates are the products of a process now called “secondary endosymbiosis” (i.e., the evolution of a chloroplast surrounded by three or four membranes resulting from the incorporation of a eukaryotic alga by a eukaryotic heterotrophic host cell). In this article, we explore the evidence for Goldschmidt’s “hopeful monster” concept and expand the scope of this theory to include the macroevolutionary emergence of organisms like Euglena and Chlorarachnion from secondary endosymbiotic events. We argue that a Neo-Goldschmidtian perspective leads to the conclusion that cell chimeras such as euglenids and dinoflagellates, which are important groups of phytoplankton in freshwater and marine ecosystems, should be interpreted as “successful monsters”. In addition, we argue that Charles Darwin had euglenoids (infusoria) in mind when he speculated on the “primordial intermediate form”, although his Proto-Euglena-hypothesis for the origin of the last common ancestor of all forms of life is no longer acceptable.