Sharply tuned cochlear nerve ensemble periodicity responses to sonic and ultrasonic frequencies

Vertebrates are able to perceive the pitch of a series of harmonics, even when the fundamental frequency has been removed from the acoustic stimulus. Neural periodicity responses corresponding to the “missing fundamental” frequency of sonic stimuli have been observed in the auditory system of several animal species, including our own. This paper examines periodic cochlear neural responses of the gerbil. Periodicity responses to both sonic and ultrasonic stimuli originate within the cochlea of this animal. Acoustic stimuli, consisting of 2–12 successive harmonic frequencies, were used to generate an ensemble cochlear nerve periodicity response that was recorded from the round window of the cochlea. This response had a frequency equal to that of the missing fundamental, and not to those of the harmonic stimuli. Forward masking of the stimuli used to produce the periodicity response was used to generate sharp tuning curves, with tip frequencies corresponding to the harmonics and not to the periodicities. The sharpness of these functions increased as the frequencies of the harmonics increased, up to at least 38 kHz. This property could be related to reception of ultrasonic vocalizations utilized by many rodent species. Accepted: 11 April 1997     

Long-term adaptation of epistatic genetic networks

Gene networks are likely to govern most traits in nature. Mutations at these genes often show functional epistatic interactions that lead to complex genetic architectures and variable fitness effects in different genetic backgrounds. Understanding how epistatic genetic systems evolve in nature remains one of the great challenges in evolutionary biology. Here we combine an analytical framework with individual-based simulations to generate novel predictions about long-term adaptation of epistatic networks. We find that relative to traits governed by independently evolving genes, adaptation with epistatic gene networks is often characterized by longer waiting times to selective sweeps, lower standing genetic variation, and larger fitness effects of adaptive mutations. This may cause epistatic networks to either adapt more slowly or more quickly relative to a nonepistatic system. Interestingly, epistatic networks may adapt faster even when epistatic effects of mutations are on average deleterious. Further, we study the evolution of epistatic properties of adaptive mutations in gene networks. Our results show that adaptive mutations with small fitness effects typically evolve positive synergistic interactions, whereas adaptive mutations with large fitness effects evolve positive synergistic and negative antagonistic interactions at approximately equal frequencies. These results provide testable predictions for adaptation of traits governed by epistatic networks and the evolution of epistasis within networks.     

An immune network inspired evolutionary algorithm for the diagnosis of Parkinson's disease

This paper presents a novel evolutionary algorithm inspired by protein/substrate binding exploited in enzyme genetic programming (EGP) and artificial immune networks. The immune network-inspired evolutionary algorithm has been developed in direct response to an application in clinical neurology, the diagnosis of Parkinson's disease. The inspiration for, and implementation of the algorithm is described and its performance to the application area considered.     

Harmonic calls and indifferent females: no preference for human consonance in an anuran

The human music faculty might have evolved from rudimentary components that occur in non-human animals. The evolutionary history of these rudimentary perceptual features is not well understood and rarely extends beyond a consideration of vertebrates that possess a cochlea. One such antecedent is a preferential response to what humans perceive as consonant harmonic sounds, which are common in many animal vocal repertoires. We tested the phonotactic response of female túngara frogs (Physalaemus pustulosus) to variations in the frequency ratios of their harmonically structured mating call to determine whether frequency ratio influences attraction to acoustic stimuli in this vertebrate that lacks a cochlea. We found that the ratio of frequencies present in acoustic stimuli did not influence female response. Instead, the amount of inner ear stimulation predicted female preference behaviour. We conclude that the harmonic relationships that characterize the vocalizations of these frogs did not evolve in response to a preference for frequency intervals with low-integer ratios. Instead, the presence of harmonics in their mating call, and perhaps in the vocalizations of many other animals, is more likely due to the biomechanics of sound production rather than any preference for ‘more musical’ sounds.     

Harmonic analysis of two-tone discharge patterns in cochlear nerve fibers

Discharges in cochlear nerve fibers evoked by low frequency phase-locked sinusoidal acoustic stimuli are synchronized to the stimulus waveform. Excitation and suppression regions of single units were explored using a stimulus composed of either a fixed intensity test tone at the characteristic frequency, a variable intensity interfering tone with a simple integer frequency relation to the characteristic frequency, or both. Compound period histograms were constructed from period histograms in response to normal and reversed polarity stimuli. Discharge patterns were characterized by Fourier components of the histogram envelopes. The two stimulus frequencies constituted the principal harmonics in the histogram envelopes and their combination accounted for observed rate changes. Suppression of the test tone harmonic as a function of interfering tone intensity was always seen; rate suppression was not. The harmonic was typically suppressed by 20–30 dB compared to the value for the test tone alone and often reached the 40–60 dB resolution limit of the experiment. Suppression plots were nearly linear on a power scale with an average slope of-0.8. The onset of suppression occurred for an interfering tone 9 dB greater on average than the test tone intensity. Information transfer through the peripheral system was described by the ratio of the principal harmonic amplitudes versus the ratio of the intensities of the two stimulus tones. These plots were nearly linear on a power scale with an average slope of 0.9. Neither the onset of suppression nor the slopes of the harmonic plots displayed strong dependence on characteristic frequency or interfering tone frequency. These features of harmonic behavior, however, are closely related to system nonlinearity. Comparison of measured harmonics to the predictions of two phenomenological models suggest the presence of complex nonlinear transformations in the peripheral auditory system.     

Impedance of the arterial system in terms of Fourier harmonic analysis of the pulse wave.

The results obtained by analysis of pulse waves by means of Fourier harmonics in healthy subjects and patients with aortic insufficiency show good agreement between input impedance of the aorta and the initial segment of the femoral bed in both groups. This means that in this region there is no marked increase in impedance, which provides a favourable background for energy transfer (blood content) in the distal direction. Impedance in healthy subjects increases in vessels of the lower extremity. In patients with aortic insufficiency there is a marked decrease in amplitude of all higher harmonic frequencies. This practically means that the second harmonic is no longer the main accumulator of energy of the pulse wave as in healthy subjects, and the same is also true, to a proportionate degree, for the third, fourth and fifth harmonics.     

Constructing Level-2 Phylogenetic Networks from Triplets

Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so, to construct such a network [24]. Here, we extend this work by showing that this problem is even polynomial time solvable for the construction of level-2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontree-like. This further strengthens the case for the use of triplet-based methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data.     

Analytical morphometry of seminiferous tubules in maturation arrest: Fourier analysis of the internal contours of tubules

Shape of seminiferous tubuli in maturation arrest, is investigated by harmonic Fourier analysis and upper degree polynomials as attempt to find morphometric parameters useful in morphological diagnosis. Inner luminal contour is considered as a closed curve in a reference system and scattered in a series of points whose coordinates are automatically calculated. Then a software named S.A.M. (Shape Analytical Morphometry) is utilized to find the Kth-order equation and calculate the best-fit curve. Moreover an ellypse is drawn with the same barycenter and axes of original curve. These three curves (real curve, best-fit curve and ellypse) are considered as periodic functions and submitted to Fourier analysis to evaluate the coefficients of the series and the spectrum of harmonics. Among 20 contributors, the subsets of greatest amplitude are selected for comparison and classification in terms of fundamental shape and its perturbations.     

Modelling spatial dynamics of fish

Our ability to model spatial distributions of fish populations is reviewed by describing the available modelling tools. Ultimate models of the individual's motivation for behavioural decisions are derived from evolutionary ecology. Mechanistic models for how fish sense and may respond to their surroundings are presented for vision, olfaction, hearing, the lateral line and other sensory organs. Models for learning and memory are presented, based both upon evolutionary optimization premises and upon neurological information processing and decision making. Functional tools for modelling behaviour and life histories can be categorized as belonging to an optimization or an adaptation approach. Among optimization tools, optimal foraging theory, life history theory, ideal free distribution, game theory and stochastic dynamic programming are presented. Among adaptation tools, genetic algorithms and the combination with artificial neural networks are described. The review advocates the combination of evolutionary and neurological approaches to modelling spatial dynamics of fish.     

Frequency following response to cochlear nuclei in cats to polycomponent sonic signals]

Under chloralose-urethane anaesthesia, by means of spectrograms and dynamic spectrograms studies have been made on frequency following response (FFR) in the cochlear nuclei of cats evoked by sonic stimulation. It was shown that FFR readily reproduces frequencies of the acoustic spectrum of separate tones and two-tonal harmonic complexes (the upper reproduced frequency in FFR - 6.0-6.5 kc/sec). The main deteils of the acoustic spectrum of the sounds of speech are also easily reproduced in FFR. Combination tones were observed in FFR during application of two-tonal harmonic complexes. The first harmonic is inhibited in FFR when combined with higher ones (the fifth or the sixth) or at certain phase angle between the first and the second harmonics ("doubling" phenomenon).     

Polynomials to model the growth of young bulls in performance tests

The use of polynomial functions to describe the average growth trajectory and covariance functions of Nellore and MA (21/32 Charolais+11/32 Nellore) young bulls in performance tests was studied. The average growth trajectories and additive genetic and permanent environmental covariance functions were fit with Legendre (linear through quintic) and quadratic B-spline (with two to four intervals) polynomials. In general, the Legendre and quadratic B-spline models that included more covariance parameters provided a better fit with the data. When comparing models with the same number of parameters, the quadratic B-spline provided a better fit than the Legendre polynomials. The quadratic B-spline with four intervals provided the best fit for the Nellore and MA groups. The fitting of random regression models with different types of polynomials (Legendre polynomials or B-spline) affected neither the genetic parameters estimates nor the ranking of the Nellore young bulls. However, fitting different type of polynomials affected the genetic parameters estimates and the ranking of the MA young bulls. Parsimonious Legendre or quadratic B-spline models could be used for genetic evaluation of body weight of Nellore young bulls in performance tests, whereas these parsimonious models were less efficient for animals of the MA genetic group owing to limited data at the extreme ages.     

Evolutionary history as a driver of ecological networks: a case study of plant–hummingbird interactions

Multiple factors drive species interactions in ecological networks, such as morphological barriers, spatio–temporal distribution, abundances and evolutionary histories of species. Novel methods are making it possible to evaluate the relative importance of each of these drivers. However, the lack of appropriate methods has prevented evaluating the extent to which interaction networks are shaped by species’ evolutionary histories. This study includes the evolutionary histories of species among the potential drivers of interactions, allowing the comparative analysis of its importance in structuring ecological networks. We hypothesized different possible phylogenetic scenarios to predict frequencies of interactions between species by combining concepts from the fields of ecological networks and ecophylogenetics. The usage of these scenarios is illustrated in a plant–hummingbird interaction network database from the Atlantic Forest, southeastern Brazil. We first evaluated which phylogenetic hypotheses better predict the observed network; subsequently, we evaluated the relative importance of species evolutionary histories, abundances, and matching on species morphologies and phenologies as drivers of their frequencies of interactions. The results suggest that the evolutionary histories of hummingbirds are more important than the species abundances in structuring the studied plant–hummingbird network but less important than the morphological and phenological matching among species. The approach developed here offers the potential to advance our understanding of the multiple factors structuring ecological networks.     

Genotype networks shed light on evolutionary constraints

An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. One can distinguish physicochemical, selective, genetic and developmental causes of such constraints. Here, I discuss these causes in three classes of system that bring forth many phenotypic traits and evolutionary innovations: regulatory circuits, macromolecules and metabolic networks. In these systems, genotypes with the same phenotype form large genotype networks that extend throughout a vast genotype space. Such genotype networks can help unify different causes of evolutionary constraints. They can show that these causes ultimately emerge from the process of development; that is, how phenotypes form from genotypes. Furthermore, they can explain important consequences of constraints, such as punctuated stasis and canalization.     

Fixed-point bifurcation analysis in biological models using interval polynomials theory

The paper proposes a systematic method for fixed-point bifurcation analysis in circadian cells and similar biological models using interval polynomials theory. The stages for performing fixed-point bifurcation analysis in such biological systems comprise (i) the computation of fixed points as functions of the bifurcation parameter and (ii) the evaluation of the type of stability for each fixed point through the computation of the eigenvalues of the Jacobian matrix that is associated with the system’s nonlinear dynamics model. Stage (ii) requires the computation of the roots of the characteristic polynomial of the Jacobian matrix. This problem is nontrivial since the coefficients of the characteristic polynomial are functions of the bifurcation parameter and the latter varies within intervals. To obtain a clear view about the values of the roots of the characteristic polynomial and about the stability features they provide to the system, the use of interval polynomials theory and particularly of Kharitonov’s stability theorem is proposed. In this approach, the study of the stability of a characteristic polynomial with coefficients that vary in intervals is equivalent to the study of the stability of four polynomials with crisp coefficients computed from the boundaries of the aforementioned intervals. The efficiency of the proposed approach for the analysis of fixed-point bifurcations in nonlinear models of biological neurons is tested through numerical and simulation experiments.     

Theory of harmonic generation in a plasma produced by the photoionization of gas atoms with electrons in the <Emphasis Type="Italic">np</Emphasis> states

For a plasma produced by the photoionization of hydrogen-like atoms with electrons in the np states, a theory is developed that describes the nonlinear plasma polarizability due to electron-ion collisions, which governs the bremsstrahlung-induced coherent harmonic generation. The effective partial collision frequencies are obtained as functions of the pump field intensity for the first four p states of hydrogen-like atoms and for the third, fifth, seventh, ninth, and eleventh harmonics. These analytic results make it possible to establish the scalings of the collision frequencies with pump field intensity, the principal quantum number, and the number of the generated harmonic. In the case of pump fields of comparatively low intensities, some qualitative differences are revealed between these scalings and the corresponding scalings obtained for the Bethe regime of suppression of the photoionization barrier in a gas of hydrogen-like atoms with electrons in the ns states.     

Steady State Detection of Chemical Reaction Networks Using a Simplified Analytical Method

Chemical reaction networks (CRNs) are susceptible to mathematical modelling. The dynamic behavior of CRNs can be investigated by solving the polynomial equations derived from its structure. However, simple CRN give rise to non-linear polynomials that are difficult to resolve. Here we propose a procedure to locate the steady states of CRNs from a formula derived through algebraic geometry methods. We have applied this procedure to define the steady states of a classic CRN that exhibits instability, and to a model of programmed cell death.     

Communication in a noisy environment: short-term acoustic adjustments and the underlying acoustic niche of a Neotropical stream-breeding frog

Acoustically active animals may show long- and short-term adaptations in acoustic traits for coping with ambient noise. Given the key role of calls in anurans’ life history, long- and short-term adaptations are expected in species inhabiting noisy habitats. However, to disentangle such adaptations is a difficult task, incipiently addressed for Neotropical frogs. We investigated if males of a stream-breeding frog (Crossodactylus schmidti) adjust call traits according to the background noise, and if the signal-to-noise ratio (SNR) varies between call harmonics and along call notes. We measured sound pressure levels of calls and noise in the field and used a fine-scale acoustic analysis to describe the signal and noise structure and test for noise-related call adjustments. The multi-note harmonic call of C. schmidti greatly varied in the spectral structure, including a trend for increasing note amplitude along the call, a wide frequency bandwidth of the 2nd harmonic, a minor call frequency modulation due to a trend for increasing note frequency within the same harmonic, and a major call frequency modulation due to the variable location of the dominant harmonic along the call. Calls had significantly higher frequencies than the noise at the range of the 1st and the 2nd call harmonics, and significantly louder sound pressure than the noise at the range of all harmonics. Males emitted the majority of call notes showing positive SNR, and though males also emitted some notes with negative SNR, when a given harmonic was negative the other harmonics in the same note did not tend to be SNR-negative. Our results indicate that male C. schmidti show short-term acoustic adjustments that make the advertisement call effective for coping with the interference of the stream-generated noise. We suggest that the call spectral plasticity serves for coping with temporary changes in the background noise, whilst we also discuss the possibility that the redundant, harmonic-structured call may have evolved to diminish masking interference on the acoustic signal by the background noise. This is the first study to uncouple noise-related acoustic adjustments and putative long-term acoustic adaptations for a Hylodidae, providing insights on behavioral plasticity and signal evolution of stream-breeding frogs.     

Circadian rhythmicity of prolactin secretion in Huntington's chorea

Prolactin circadian secretion has been studied in 16 males and in 8 females with Huntington's Chorea, in order to evaluate changes of the hormone's titres and of their periodicity in a condition where alterations of neurotransmission have been documented. Prolactin levels have been found normal, enhanced and low levels have been observed in one male case. Sleep connected surge has been found to be present in all cases. A harmonic analysis of periodical changes has been performed by a Fourier's cosines series. The changes in the occurence of different harmonic frequencies in respect to normal controls are not significant. No correlation could be drawn among clinical indices, hormone levels and the feature of the occurring harmonics.     

Data and theory point to mainly additive genetic variance for complex traits

The relative proportion of additive and non-additive variation for complex traits is important in evolutionary biology, medicine, and agriculture. We address a long-standing controversy and paradox about the contribution of non-additive genetic variation, namely that knowledge about biological pathways and gene networks imply that epistasis is important. Yet empirical data across a range of traits and species imply that most genetic variance is additive. We evaluate the evidence from empirical studies of genetic variance components and find that additive variance typically accounts for over half, and often close to 100%, of the total genetic variance. We present new theoretical results, based upon the distribution of allele frequencies under neutral and other population genetic models, that show why this is the case even if there are non-additive effects at the level of gene action. We conclude that interactions at the level of genes are not likely to generate much interaction at the level of variance.