Small tumor virus genomes are integrated near nuclear matrix attachment regions in transformed cells.

More than 15% of human cancers have a viral etiology. In benign lesions induced by the small DNA tumor viruses, viral genomes are typically maintained extrachromosomally. Malignant progression is often associated with viral integration into host cell chromatin. To study the role of viral integration in tumorigenesis, we analyzed the positions of integrated viral genomes in tumors and tumor cell lines induced by the small oncogenic viruses, including the high-risk human papillomaviruses, hepatitis B virus, simian virus 40, and human T-cell leukemia virus type 1. We show that viral integrations in tumor cells lie near cellular sequences identified as nuclear matrix attachment regions (MARs), while integrations in nonneoplastic cells show no significant correlation with these regions. In mammalian cells, the nuclear matrix functions in gene expression and DNA replication. MARs play varied but poorly understood roles in eukaryotic gene expression. Our results suggest that integrated tumor virus genomes are subject to MAR-mediated transcriptional regulation, providing insight into mechanisms of viral carcinogenesis. Furthermore, the viral oncoproteins serve as invaluable tools for the study of mechanisms controlling cellular growth. Similarly, our demonstration that integrated viral genomes may be subject to MAR-mediated transcriptional effects should facilitate elucidation of fundamental mechanisms regulating eukaryotic gene expression.

Intensity-invariance of fine time structure in basilar-membrane click responses: implications for cochlear mechanics.

Basilar-membrane and auditory-nerve responses to impulsive acoustic stimuli, whether measured directly in response to clicks or obtained indirectly using cross- or reverse-correlation and/or Fourier analysis, manifest a striking symmetry: near-invariance with stimulus intensity of the fine time structure of the response over almost the entire dynamic range of hearing. This paper explores the origin and implications of this symmetry for cochlear mechanics. Intensity-invariance is investigated by applying the EQ-NL theorem [de Boer, Aud. Neurosci. 3, 377-388 (1997)] to define a family of linear cochlear models in which the strength of the active force generators is controlled by a real-valued, intensity-dependent parameter, gamma (with 0 < or = gamma < or = 1). The invariance of fine time structure is conjectured to imply that as gamma is varied the poles of the admittance of the cochlear partition remain within relatively narrow bands of the complex plane oriented perpendicular to the real frequency axis. Physically, the conjecture implies that the local resonant frequencies of the cochlear partition are nearly independent of intensity. Cochlear-model responses, computed by extending the model obtained by solution of the inverse problem in squirrel monkey at low sound levels [Zweig, J. Acoust. Soc. Am. 89, 1229-1254 (1991)] with three different forms of the intensity dependence of the partition admittance, support the conjecture. Intensity-invariance of cochlear resonant frequencies is shown to be consistent with the well-known "half-octave shift," describing the shift with intensity in the peak (or best) frequency of the basilar-membrane frequency response. Shifts in best frequency do not arise locally, via changes in the underlying resonant frequencies of the partition, but globally through the intensity dependence of the driving pressure. Near-invariance of fine time structure places strong constraints on the mechanical effects of force generation by outer hair cells. In particular, the symmetry requires that the feedback forces generated by outer hair cells (OHCs) not significantly affect the natural resonant frequencies of the cochlear partition. These results contradict many, if not most, cochlear models, in which OHC forces produce significant changes in the reactance and resonant frequencies of the partition.

Frequency glides in click responses of the basilar membrane and auditory nerve: their scaling behavior and origin in traveling-wave dispersion.

Frequency modulations (or glides), reported in impulse responses of both the auditory nerve and the basilar membrane, represent a change over time in the instantaneous frequency of oscillation of the response waveform. Although the near invariance of glides with stimulus intensity indicates that they are not the consequence of nonlinear or active processes in the inner ear, their origin has remained otherwise obscure. This paper combines theory with experimental data to explore the basic phenomenology of glides. When expressed in natural dimensionless form, glides are shown to have a universal form nearly independent of cochlear location for characteristic frequencies (CFs) above approximately 1.5 kHz (the "scaling region"). In the apex of the cochlea, by contrast, glides appear to depend strongly on CF. In the scaling region, instantaneous-frequency trajectories are shown to be approximately equal to the "inverse group delays" of basilar-membrane transfer functions measured at the same locations. The inverse group delay, obtained by functionally inverting the transfer-function group-delay-versus-frequency curve, specifies the frequency component of a broadband stimulus expected to be driving the cochlear partition at the measurement point as a function of time. The approximate empirical equality of the two functions indicates that glides are closely related to cochlear traveling-wave dispersion and suggests that they originate primarily through the time dependence of the effective driving pressure force at the measurement location. Calculations in a one-dimensional cochlear model based on solution to the inverse problem in squirrel monkey [Zweig, J. Acoust. Soc. Am. 89, 1229-1254 (1991)] support this conclusion. In contrast to previous models for glides, which locate their origin in the differential build-up and decay of multiple micromechanical resonances local to each radial cross section of the organ of Corti, the model presented here identifies glides as the global consequence of the dispersive character of wave propagation in the cochlea.

Distortion-product source unmixing: a test of the two-mechanism model for DPOAE generation.

This paper tests key predictions of the "two-mechanism model" for the generation of distortion-product otoacoustic emissions (DPOAEs). The two-mechanism model asserts that lower-sideband DPOAEs constitute a mixture of emissions arising not simply from two distinct cochlear locations (as is now well established) but, more importantly, by two fundamentally different mechanisms: nonlinear distortion induced by the traveling wave and linear coherent reflection off pre-existing micromechanical impedance perturbations. The model predicts that (1) DPOAEs evoked by frequency-scaled stimuli (e.g., at fixed f2/f1) can be unmixed into putative distortion- and reflection-source components with the frequency dependence of their phases consistent with the presumed mechanisms of generation; (2) The putative reflection-source component of the total DPOAE closely matches the reflection-source emission (e.g., low level stimulus-frequency emission) measured at the same frequency under similar conditions. These predictions were tested by unmixing DPOAEs into components using two completely different methods: (a) selective suppression of the putative reflection source using a third tone near the distortion-product frequency and (b) spectral smoothing (or, equivalently, time-domain windowing). Although the two methods unmix in very different ways, they yield similar DPOAE components. The properties of the two DPOAE components are consistent with the predictions of the two-mechanism model.

Middle ear pathology can affect the ear-canal sound pressure generated by audiologic earphones.

OBJECTIVE: To determine how the ear-canal sound pressures generated by earphones differ between normal and pathologic middle ears. DESIGN: Measurements of ear-canal sound pressures generated by the Etymtic Research ER-3A insert earphone in normal ears (N = 12) were compared with the pressures generated in abnormal ears with mastoidectomy bowls (N = 15), tympanostomy tubes (N = 5), and tympanic-membrane perforations (N = 5). Similar measurements were made with the Telephonics TDH-49 supra-aural earphone in normal ears (N = 10) and abnormal ears with mastoidectomy bowls (N = 10), tympanostomy tubes (N = 4), and tympanic-membrane perforations (N = 5). RESULTS: With the insert earphone, the sound pressures generated in the mastoid-bowl ears were all smaller than the pressures generated in normal ears; from 250 to 1000 Hz the difference in pressure level was nearly frequency independent and ranged from -3 to -15 dB; from 1000 to 4000 Hz the reduction in level increased with frequency and ranged from -5 dB to -35 dB. In the ears with tympanostomy tubes and perforations the sound pressures were always smaller than in normal ears at frequencies below 1000 Hz; the largest differences occurred below 500 Hz and ranged from -5 to -25 dB. With the supra-aural earphone, the sound pressures in ears with the three pathologic conditions were more variable than those with the insert earphone. Generally, sound pressures in the ears with mastoid bowls were lower than those in normal ears for frequencies below about 500 Hz; above about 500 Hz the pressures showed sharp minima and maxima that were not seen in the normal ears. The ears with tympanostomy tubes and tympanic-membrane perforations also showed reduced ear-canal pressures at the lower frequencies, but at higher frequencies these ear-canal pressures were generally similar to the pressures measured in the normal ears. CONCLUSIONS: When the middle ear is not normal, ear-canal sound pressures can differ by up to 35 dB from the normal-ear value. Because the pressure level generally is decreased in the pathologic conditions that were studied, the measured hearing loss would exaggerate substantially the actual loss in ear sensitivity. The variations depend on the earphone, the middle ear pathology, and frequency. Uncontrolled variations in ear-canal pressure, whether caused by a poor earphone-to-ear connection or by abnormal middle ear impedance, could be corrected with audiometers that measure sound pressures during hearing tests.

Acoustic mechanisms that determine the ear-canal sound pressures generated by earphones.

In clinical measurements of hearing sensitivity, a given earphone is assumed to produce essentially the same sound-pressure level in all ears. However, recent measurements [Voss et al., Ear and Hearing (in press)] show that with some middle-ear pathologies, ear-canal sound pressures can deviate by as much as 35 dB from the normal-ear value; the deviations depend on the earphone, the middle-ear pathology, and frequency. These pressure variations cause errors in the results of hearing tests. Models developed here identify acoustic mechanisms that cause pressure variations in certain pathological conditions. The models combine measurement-based Thévenin equivalents for insert and supra-aural earphones with lumped-element models for both the normal ear and ears with pathologies that alter the ear's impedance (mastoid bowl, tympanostomy tube, tympanic-membrane perforation, and a "high-impedance" ear). Comparison of the earphones' Thévenin impedances to the ear's input impedance with these middle-ear conditions shows that neither class of earphone acts as an ideal pressure source; with some middle-ear pathologies, the ear's input impedance deviates substantially from normal and thereby causes abnormal ear-canal pressure levels. In general, for the three conditions that make the ear's impedance magnitude lower than normal, the model predicts a reduced ear-canal pressure (as much as 35 dB), with a greater pressure reduction with an insert earphone than with a supra-aural earphone. In contrast, the model predicts that ear-canal pressure levels increase only a few dB when the ear has an increased impedance magnitude; the compliance of the air-space between the tympanic membrane and the earphone determines an upper limit on the effect of the middle-ear's impedance increase. Acoustic leaks at the earphone-to-ear connection can also cause uncontrolled pressure variations during hearing tests. From measurements at the supra-aural earphone-to-ear connection, we conclude that it is unusual for the connection between the earphone cushion and the pinna to seal effectively for frequencies below 250 Hz. The models developed here explain the measured pressure variations with several pathologic ears. Understanding these mechanisms should inform the design of more accurate audiometric systems which might include a microphone that monitors the ear-canal pressure and corrects deviations from normal.

Interrelations among distortion-product phase-gradient delays: their connection to scaling symmetry and its breaking.

Distortion-product-otoacoustic-emission (DPOAE) phase-versus-frequency functions and corresponding phase-gradient delays have received considerable attention because of their potential for providing information about mechanisms of emission generation, cochlear wave latencies, and characteristics of cochlear tuning. The three measurement paradigms in common use (fixed-f1, fixed-f2, and fixed-f2/f1) yield significantly different delays, suggesting that they depend on qualitatively different aspects of cochlear mechanics. In this paper, theory and experiment are combined to demonstrate that simple phenomenological arguments, which make no detailed mechanistic assumptions concerning the underlying cochlear mechanics, predict relationships among the delays that are in good quantitative agreement with experimental data obtained in guinea pigs. To understand deviations between the simple theory and experiment, a general equation is found that relates the three delays for any deterministic model of DPOAE generation. Both model-independent and exact, the general relation provides a powerful consistency check on the measurements and a useful tool for organizing and understanding the structure in DPOAE phase data (e.g., for interpreting the relative magnitudes and intensity-dependencies of the three delays). Analysis of the general relation demonstrates that the success of the simple, phenomenological approach can be understood as a consequence of the mechanisms of emission generation and the approximate local scaling symmetry of cochlear mechanics. The general relation is used to quantify deviations from scaling manifest in the measured phase-gradient delays; the results indicate that deviations from scaling are typically small and that both linear and nonlinear mechanisms contribute significantly to these deviations. Intensity-dependent mechanisms contributing to deviations from scaling include cochlear-reflection and wave-interference effects associated with the mixing of distortion- and reflection-source emissions (as in DPOAE fine structure). Finally, the ratio of the fixed-f1 and fixed-f2 phase-gradient delays is shown to follow from the choice of experimental paradigm and, in the scaling limit, contains no information about cochlear physiology whatsoever. These results cast considerable doubt on the theoretical basis of recent attempts to use relative DPOAE phase-gradient delays to estimate the bandwidths of peripheral auditory filters.

Evoked otoacoustic emissions arise by two fundamentally different mechanisms: a taxonomy for mammalian OAEs.

Otoacoustic emissions (OAEs) of all types are widely assumed to arise by a common mechanism: nonlinear electromechanical distortion within the cochlea. In this view, both stimulus-frequency (SFOAEs) and distortion-product emissions (DPOAEs) arise because nonlinearities in the mechanics act as "sources" of backward-traveling waves. This unified picture is tested by analyzing measurements of emission phase using a simple phenomenological description of the nonlinear re-emission process. The analysis framework is independent of the detailed form of the emission sources and the nonlinearities that produce them. The analysis demonstrates that the common assumption that SFOAEs originate by nonlinear distortion requires that SFOAE phase be essentially independent of frequency, in striking contradiction with experiment. This contradiction implies that evoked otoacoustic emissions arise by two fundamentally different mechanisms within the cochlea. These two mechanisms (linear reflection versus nonlinear distortion) are described and two broad classes of emissions--reflection-source and distortion-source emissions--are distinguished based on the mechanisms of their generation. The implications of this OAE taxonomy for the measurement, interpretation, and clinical use of otoacoustic emissions as noninvasive probes of cochlear function are discussed.

The origin of periodicity in the spectrum of evoked otoacoustic emissions.

Current models of evoked otoacoustic emissions explain the striking periodicity in their frequency spectra by suggesting that it originates through the reflection of forward-traveling waves by a corresponding spatial corrugation in the mechanics of the cochlea. Although measurements of primate cochlear anatomy find no such corrugation, they do indicate a considerable irregularity in the arrangement of outer hair cells. It is suggested that evoked emissions originate through a novel reflection mechanism, representing an analogue of Bragg scattering in nonuniform, disordered media. Forward-traveling waves reflect off random irregularities in the micromechanics of the organ of Corti. The tall, broad peak of the traveling wave defines a localized region of coherent reflection that sweeps along the organ of Corti as the frequency is varied monotonically. Coherent scattering occurs off irregularities within the peak with spatial period equal to half the wavelength of the traveling wave. The phase of the net reflected wave rotates uniformly with frequency at a rate determined by the wavelength of the traveling wave in the region of its peak. Interference between the backward-traveling wave and the stimulus tone creates the observed spectral periodicity. Ear-canal measurements are related to cochlear mechanics by assuming that the transfer characteristics of the middle ear vary slowly with frequency compared to oscillations in the emission spectrum. The relationship between cochlear mechanics at low sound levels and the frequency dependence of evoked emissions is made precise for one-dimensional models of cochlear mechanics. Measurements of basilar-membrane motion in the squirrel monkey are used to predict the spectral characteristics of their emissions. And conversely, noninvasive measurements of evoked otoacoustic emissions are used to predict the width and wavelength of the peak of the traveling wave in humans.

Noninvasive measurement of the cochlear traveling-wave ratio.

The microstructure of threshold hearing curves and the frequency spectra of evoked otoacoustic emissions both often evince a roughly periodic series of maxima and minima. Current models for the generation of otoacoustic emissions explain the observed spectral regularity by supposing that since the cochlea maps frequency into position the spectral periodicity mirrors a spatial oscillation in the mechanics of the organ of Corti. In this view emissions are generated when forward-traveling waves reflect from periodic corrugations in the mechanics, suggesting that the amplitude of the cochlear waves at the stapes--should manifest pronounced maxima and minima with a corresponding periodicity. This paper describes measurements of stimulus-frequency emissions, establishes their analyticity properties, and uses them to explore the spatial distribution of mechanical inhomogeneities (emission "generators") in the human cochlea. The approximate form and frequency dependence of the cochlear traveling-wave ratio are determined noninvasively. The amplitude of the empirical traveling-wave ratio is a slowly varying, nonperiodic function of frequency, suggesting that the distribution of inhomogeneities is uncorrelated with the periodicity found in the threshold microstructure. The observed periodicities arise predominantly from the cyclic variation in relative phase between the forward- and backward-traveling waves at the stapes.

Middle-ear phenomenology: the view from the three windows.

To provide a common ground for the comparison between theory and experiment, this paper presents a framework for the phenomenological description of middle-ear mechanics. The framework defines those measurements sufficient to characterize the transduction properties of the middle ear and its components. Phenomenological equations are represented in the form of an equivalent electrical circuit that can be used to deduce testable relations among measurable quantities. Two applications are then discussed. First, the classical concept of the middle-ear transformer ratio is generalized to include any effects of eardrum flexion or nonrotational ossicular motion. Middle-ear models predict that the resulting transformer ratios vary considerably with frequency. Second, the conditions under which the topology of existing circuit analogs satisfactorily approximates middle-ear mechanics are given. Most middle-ear models cannot be used to correctly predict the absolute pressures in the cochlea.

Analyzing reverse middle-ear transmission: noninvasive Gedankenexperiments.

The phenomenological framework outlined in the companion paper [C. A. Shera and G. Zweig, J. Acoust. Soc. Am. 92, 1356-1370 (1992)] characterizes both forward and reverse transmission through the middle ear. This paper illustrates its use in the analysis of noninvasive measurements of middle-ear and cochlear mechanics. A cochlear scattering framework is developed for the analysis of combination-tone and other experiments in which acoustic distortion products are used to drive the middle ear "in reverse." The framework is illustrated with a simple psychophysical Gedankenexperiment analogous to the neurophysiological experiments of P. F. Fahey and J. B. Allen [J. Acoust. Soc. Am. 77, 599-612 (1985)].

An empirical bound on the compressibility of the cochlea.

Effects of a possible inner-ear compressibility on middle-ear transfer functions are explored and a small upper bound on the magnitude of that compressibility established. Consequently. the traditional two-port representation of middle-ear mechanics remains valid to within a few percent. If the compressibility of the cochlea is small but finite, a simple phenomenological model of that compressibility correctly predicts hearing thresholds in the "middleless" ear at low frequencies. Experiments to establish the value of cochlear compressibility and to explore further its possible contributions to residual hearing in patients with missing or disarticulated middle-ear ossicles are suggested.

Phenomenological characterization of eardrum transduction.

A phenomenological description of the transduction effected by the eardrum is presented. That description is provided by a transfer matrix, whose elements define those measurements sufficient to characterize eardrum transduction. Causality provides constraints on the matrix elements. In addition, measurements of the matrix elements can determine whether they satisfy constraints imposed by minimum-phase behavior and the principle of reciprocity. Those constraints may be used either to reduce the number of measurements necessary to characterize the eardrum or to check the consistency of measurements that overdetermine the system. Within its region of validity, the transfer matrix of the eardrum provides a common ground for the comparison between theory and experiment. As an example, a simple model for the transduction characteristics of the eardrum, defined completely in terms of measurable quantities, is presented.

A symmetry suppresses the cochlear catastrophe.

When the independent spatial variable is defined appropriately, the empirical finding that the phase of the cochlear input impedance is small [Lynch et al., J. Acoust. Soc. Am. 72, 108-130 (1982)] is shown to imply that the wavelength of the pressure wave in the cochlea changes slowly with position near the stapes. As a result, waves traveling in either direction through the basal turn undergo little reflection, and the transfer of energy between the middle and inner ears remains efficient at low frequencies. The slow variation of the wavelength implies that the series impedance Z and shunt admittance Y of the cochlear transmission line are approximately proportional at low frequencies and thus requires that the width of the basilar membrane and the cross-sectional areas of the cochlear scalae taper in opposite directions. Maintenance of the symmetry between Z and Y is both necessary and sufficient to ensure that the spatial derivative of the wavelength, and hence the phase of the cochlear input impedance, remains small. Although introduced in another context, the model of Zweig ["Finding the impedance of the organ of Corti," J. Acoust. Soc. Am. 89, 1229-1254 (1991)] manifests the symmetry between Z and Y. In other transmission-line models of cochlear mechanics, however, that symmetry is absent, and the spatial derivative of the wavelength diverges at low frequencies--the "cochlear catastrophe." Those models therefore contradict the impedance measurements and predict little transfer of energy between the middle and inner ears.

Reflection of retrograde waves within the cochlea and at the stapes.

A number of authors [de Boer and Viergever, Hear. Res. 13, 101-112 (1984); de Boer et al., in Peripheral Auditory Mechanisms (Springer-Verlag, Berlin, 1986); Hear. Res. 23, 1-7 (1986); Viergever, in Auditory Frequency Selectivity (Plenum, New York, 1986), pp. 31-38; Kaernbach et al., J. Acoust. Soc. Am. 81, 408-411 (1987)] have argued that backward-traveling waves, in striking contrast to waves traveling forward towards the helicotrema, suffer appreciable reflection as they move through the basal turns of the cochlea. Such reflection, if present, would have important consequences for understanding the nature and strength of otoacoustic emissions. The apparent asymmetry in reflection of cochlear waves is shown, however, to be an artifact of the boundary condition those authors impose at the stapes: conventional cochlear models are found not to generate reflections of waves traveling in either direction even when the wavelength changes rapidly and the WKB approximation breaks down. Although backward-traveling waves are not reflected by the secular variation of the geometrical and mechanical characteristics of the cochlea, they are reflected when they reach the stapes. The magnitude of that boundary reflection is computed for the cat and shown to be a large, rapidly varying function of frequency.