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PubMed1993

Detection and identification of a single modulated carrier in a complex sound.

Hall and Grose [J. Acoust. Soc. Am. 90, 3028-3035 (1991)] reported that subjects had difficulty in deciding which carrier in a two-carrier complex sound was modulated. The present experiments examined how the ability to identify a single modulated carrier was affected by the number of carriers in the complex and by harmonicity. Initially, thresholds were measured for detecting amplitude modulation of a single carrier in a complex sound. Thresholds were higher when that carrier was one of the inner carriers in a six-carrier harmonic or inharmonic complex than when it formed part of a two-carrier complex. Thresholds were only slightly, if at all, higher when the modulated carrier was varied randomly from trial to trial than when its frequency was fixed within a block of trials. Next, subjects were required to decide whether the frequency of a single modulated carrier (with a suprathreshold modulation depth) in a complex sound was the same as or different from the frequency of a probe composed of a single modulated carrier. They generally performed well above chance. Performance was not greatly affected by whether the probe was presented before or after the complex, but was generally slightly better for a modulation depth of 100% than for a depth of 50%. Randomly varying the level of each carrier in the complexes from one stimulus to the next produced only a slight impairment of performance, indicating that short-term across-frequency differences in level were not used to identify the modulated carrier in experiment 2. Overall, performance was best for the six-carrier harmonic complex, less good for the six-carrier inharmonic complex, and worst for the two-carrier complex. The results are interpreted in terms of perceptual grouping.

Auditory Perception↗
PubMed1994

Effects of carrier frequency and background noise on the detection of mixed modulation.

This article is concerned with the mechanisms underlying the detection of amplitude modulation (AM), frequency modulation (FM), and mixed modulation (MM), i.e., simultaneously occurring AM and FM. In a previous study [B. C. J. Moore and A. Sek, J. Acoust. Soc. Am. 92, 3119-3131 (1992)], psychometric functions were measured for the detection of AM alone and FM alone, using a 10-Hz modulation rate and a 1-kHz carrier frequency. Detectability was then measured for combined AM and FM, with modulation depths selected so that each type of modulation would be equally detectable if presented alone. The detectability of the combined AM and FM was better than would be predicted if the two types of modulation were coded completely independently. Significant effects of relative modulator phase were found when detectability was relatively high, but these effects were not correctly predicted by either of two excitation-pattern models considered. The first experiment reported here was similar to the earlier experiment, but performance was compared for carrier frequencies of 1 and 6 kHz; at the latter frequency, neural synchrony to the stimulus fine structure (phase locking) does not occur. The results at both carrier frequencies were similar to those of our earlier experiment, suggesting that the presence or absence of phase-locking information plays little role in the detection of MM. The second experiment was again similar, but bands of noise were used to mask selectively either the upper or lower side of the excitation pattern of the modulated carrier. The phase effects in this case were in the direction predicted by excitation pattern models. The overall pattern of the results could be predicted reasonably well using a multichannel excitation pattern model based on the assumption that listeners use an unweighted sum of decision variables across all suprathreshold channels with a positive signal-to-noise ratio.

Auditory Perception↗
PubMed1996

Effects of masker gating for signal detection in unmodulated and modulated bandlimited noise.

Thresholds for a 400-ms 1000-Hz pure-tone signal were obtained as a function of masking noise bandwidth for unmodulated and square wave modulated masking noise. Rates of modulation were 10 and 40 Hz. Noise bandwidths were 128 Hz, 387 Hz, 921 Hz, and 1505 Hz. The masking noise was either continuous or gated on and off with the signal. In general, signal thresholds were relatively constant as a function of noise bandwidth in unmodulated noise, and improved as a function of increasing noise bandwidth in modulated noise. Noise gating had little or no effect on signal threshold in unmodulated noise. At the 10-Hz modulation rate, signal thresholds were somewhat higher in gated than in continuous noise at relatively narrow noise bandwidths, but thresholds were similar in gated and continuous noise for relatively wide noise bandwidths. At bandwidths of 387, 921, and 1505 Hz, comodulation masking release (CMR) was calculated as the unmodulated noise threshold minus the modulated noise threshold, corrected by the difference between the unmodulated noise threshold and the modulated noise threshold at the 128-Hz bandwidths. At wide masker bandwidth, CMRs were higher for gated noise than for continuous noise. This was due almost entirely to the threshold gating effect found in the 128-Hz bandwidth condition. These results suggested that there was a within-channel effect for gated noise thresholds to be higher than continuous noise thresholds, but essentially no across-channel effect of gating. At the 40-Hz modulation rate, signal thresholds were similar for gated and continuous noise at all noise bandwidths. There was a very small but significant' effect for the gated noise threshold to be lower than the continuous noise threshold at the widest noise bandwidth. It was speculated that this effect may be related to a decrease in sensitivity to modulation with continuous stimulation. In general, effects of gating appear to be small or absent for across-channel masking release in broadband modulated masking noise.

Adult↗
PubMed1997

A comparison of detection and discrimination of temporal asymmetry in amplitude modulation.

Two compound experiments were performed to compare the detection of amplitude modulation with the discrimination of modulator shape when the modulators have strong temporal asymmetry. In experiment 1, an adaptive procedure was used to measure detection and discrimination as a function of modulation frequency from 4 to 400 Hz. In experiment 2, the method of constant stimuli was used to measure psychometric functions for detection and discrimination at one modulation frequency, 8 Hz. The asymmetric modulators were time-reversed pairs. Thus their envelope spectra are identical and models based on the envelope spectrum would predict no effect of asymmetry on detection or discrimination at any modulation depth. The detection results show, as predicted, that the direction of asymmetry does not affect the detectability of modulation in either experiment. In contrast, the discrimination results show that direction of asymmetry is readily discriminable for modulation frequencies less than about 50 Hz, indicating that envelope-spectrum models will require modification if they are to be extended to include discrimination of temporal asymmetry.

Auditory Perception↗
PubMed1999

Dual temporal pitch percepts from acoustic and electric amplitude-modulated pulse trains.

Two experiments examined the perception of unmodulated and amplitude-modulated pulse trains by normally hearing listeners and cochlear implantees. Four normally hearing subjects listened to acoustic pulse trains, which were band-pass filtered between 3.9 and 5.3 kHz. Four cochlear implantees, all postlinguistically deaf users of the Mini System 22 implant, listened to current pulse trains produced at a single electrode position. In the first experiment, a set of nine loudness-balanced unmodulated stimuli with rates between 60 and 300 Hz were presented in a multidimensional scaling task. The resultant stimulus spaces for both subject groups showed a single dimension associated with the rate of the stimuli. In the second experiment, a set of ten loudness-balanced modulated stimuli was constructed, with carrier rates between 140 and 300 Hz, and modulation rates between 60 and 150 Hz. The modulation rates were integer submultiples of the carrier rates, and each modulation period consisted of one higher-intensity pulse and one or more identical lower-intensity pulses. The modulation depth of each stimulus was adjusted so that its pitch was judged to be higher or lower 50% of the time than that of an unmodulated pulse train having a rate equal to the geometric mean of the carrier and modulation rates. A multidimensional scaling task with these ten stimuli resulted in two-dimensional stimulus spaces, with dimensions corresponding to carrier and modulation rates. A further investigation with one normally hearing subject showed that the perceptual weighting of the two dimensions varied systematically with modulation depth. It was concluded that, when filtered appropriately, acoustic pulse trains can be used to produce percepts in normal listeners that share common features with those experienced by subjects listening through one channel of a cochlear implant, and that the central auditory system can extract two temporal patterns arising from the same cochlear location.

Acoustics↗
PubMed1999

Vocal production mechanisms in the budgerigar (Melopsittacus undulatus): the presence and implications of amplitude modulation.

In this paper acoustic evidence is presented for the presence of amplitude modulation in budgerigar (Melopsittacus undulatus) contact calls and learned English vocalizations. Previously, acoustic analyses of budgerigar vocalizations have consisted solely of visual inspection of spectrograms or power spectra (derived from Fourier transformation). Such analyses have led researchers to conclude that budgerigar vocalizations are primarily frequency-modulated, harmonic vocalizations. Although budgerigar calls have been shown to contain regions that are modulated in amplitude, the implications of this fact have been largely ignored. Amplitude modulation, the nonlinear interaction between two separate signals that results in the creation of new, heterodyne (sum and difference) frequencies, can produce a very complex Fourier spectrum that may resemble that produced by a harmonic vocalization. In this paper, the acoustic principles necessary for identifying amplitude modulation present in signals are outlined, and followed by data demonstrating that amplitude modulation is a prominent feature not only of natural budgerigar contact calls, but also of their learned English vocalizations. It is illustrated how analyzing a vocalization that contains amplitude modulation as if it were harmonic can result in misinterpretations of the acoustic and physical properties of the sound and sound source. The implications of amplitude modulation for studies of the ontogenetic, physical, and neural basis of budgerigar vocalizations are discussed, and a potential model for how the budgerigar syrinx may function to produce amplitude modulation is proposed.

Animals↗
PubMed2003

Identification of a site in GluR1 and GluR2 that is important for modulation of deactivation and desensitization.

The alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype of ionotropic glutamate receptors consists of rapidly gating ion channels. Positive modulation of channel gating may slow gating kinetics through at least two distinct mechanisms, evidenced by the predominant slowing of either the rate of receptor desensitization or the rate of offset after agonist withdrawal (deactivation). This study compares the actions of two positive allosteric modulators [cyclothiazide, which modulates desensitization, and 1-(1,4-benzodioxan-6-ylcarbonyl)piperidine (CX546), which modulates deactivation] in a mutant shown previously to impede modulation by cyclothiazide. These experiments test the hypothesis that the point mutation, GluR1(S493T), would also cause a loss of modulation by CX546. Wild-type GluR1 through -4 receptors were modulated by CX546, as assayed by the potentiation of steady-state currents in the Xenopus laevis oocyte expression system. CX546 potentiated steady-state currents of both splice isoforms of GluR1. Modulation by CX546 was completely abolished in GluR1(S493T) and its homolog, GluR2(S497T), although this mutation did not affect apparent agonist affinity in the absence of CX546. Thus, the GluR1(S493T) mutation has a similar impairment of modulation by either cyclothiazide or CX546, indicating that some residues at the subunit interface of glutamate receptors play an important role in channel deactivation and desensitization.

Amino Acid Substitution↗
PubMed2003

A family of highly selective allosteric modulators of the metabotropic glutamate receptor subtype 5.

We have identified a family of highly selective allosteric modulators of the group I metabotropic glutamate receptor subtype 5 (mGluR5). This family of closely related analogs exerts a spectrum of effects, ranging from positive to negative allosteric modulation, and includes compounds that do not themselves modulate mGluR5 agonist activity but rather prevent other family members from exerting their modulatory effects. 3,3'-Difluorobenzaldazine (DFB) has no agonist activity, but it acts as a selective positive allosteric modulator of human and rat mGluR5. DFB potentiates threshold responses to glutamate, quisqualate, and 3,5-dihydroxyphenylglycine in fluorometric Ca2+ assays 3- to 6-fold, with EC50 values in the 2 to 5 microM range, and at 10 to 100 microM, it shifts mGluR5 agonist concentration-response curves approximately 2-fold to the left. The analog 3,3'-dimethoxybenzaldazine (DMeOB) acts as a negative modulator of mGluR5 agonist activity, with an IC50 of 3 microM in fluorometric Ca2+ assays, whereas the analog 3,3'-dichlorobenzaldazine (DCB) does not exert any apparent modulatory effect on mGluR5 activity. However, DCB seems to act as an allosteric ligand with neutral cooperativity, preventing the positive allosteric modulation of mGluRs by DFB as well as the negative modulatory effect of DMeOB. None of these analogs affects binding of [3H]quisqualate to the orthosteric (glutamate) site, but they do inhibit [3H]3-methoxy-5-(2-pyridinylethynyl)pyridine binding to the site for 2-methyl-6-(phenylethynyl)-pyridine, a previously identified negative allosteric modulator. With the use of these compounds, we provide evidence that allosteric sites on GPCRs can respond to closely related ligands with a range of pharmacological activities from positive to negative modulation as well as to neutral competition of this modulation.

Allosteric Regulation↗
PubMed2003

Distinct roles of P2X receptors in modulating glutamate release at different primary sensory synapses in rat spinal cord.

Using spinal cord slice preparations and patch-clamp recordings in lamina II and lamina V regions, we tested a hypothesis that P2X receptor subtypes differentially modulate glutamate release from primary afferent terminals innervating different sensory regions. We found that activation of P2X receptors by alpha,beta-methylene-ATP increased glutamate release onto >80% of DH neurons in both lamina regions. However, two distinct types of modulation, a transient and a long-lasting enhancement of glutamate release were observed. In lamina II recordings, >70% of the modulation was transient. In contrast, P2X receptor-mediated modulation was always long-lasting in lamina V. Pharmacologically, both transient and long-lasting types of modulation were blocked by 10 microM pyridxal-phosphate-6-azophenyl-2',4'-disulphonic acid tetrasodium, a broad-spectrum P2X receptor antagonist. Transient modulation was not observed in the presence of 1 microM trinitrophenyl-ATP (TNP-ATP), a subtype-selective P2X receptor antagonist, suggesting that homomeric P2X3 receptors may be involved in the transient modulation in lamina II. The long-lasting modulation remained in the presence of 1 microM TNP-ATP. Selective removal of P2X3-expressing afferent terminals by the targeting toxin saporin-conjugated isolectin B4 or surgical removal of superficial DH did not affect P2X receptor-mediated long-lasting modulation in lamina V. Taken together, these results suggest that P2X receptor subtypes play distinct roles in sensory processing in functionally different sensory regions.

Adenosine Triphosphate↗
PubMed1997

Ion currents and mechanisms of modulation in the radula opener muscles of Aplysia.

Ion currents and mechanisms of modulation in the radula opener muscles of Aplysia. J. Neurophysiol. 78: 2372-2387, 1997. Numerous studies of plasticity in the feeding behavior of Aplysia have shown that substantial plasticity is due to peripheral neuromodulation of the feeding musculature. Extensive previous work focusing on the accessory radula closer (ARC) muscle has led to the realization that a major function of the modulation in that muscle may be to ensure efficient coordination between its contractions and those of its antagonist muscles. For a more complete understanding, therefore, we must study these muscles also. Here we have studied the radula opener muscles I7-I10. Using single isolated muscle fibers under voltage clamp, we have characterized ion currents gated by voltage and by the physiological contraction-inducing neurotransmitter acetylcholine (ACh) and the effects of the physiological modulators serotonin, myomodulins A and B, and FMRFamide. Our results explain significant aspects of the electrophysiological behavior of the whole opener muscles, as well as why the opener and ARC muscles behave similarly in many ways yet differently in some key respects. Opener muscles express four types of K currents: inward rectifier, A-type [IK(A)], delayed rectifier [IK(V)], and Ca2+-activated [IK(Ca)]. They also express an L-type Ca current [ICa] and a leakage current. ACh activates a positive-reversing cationic current [IACh(cat)] and a negative-reversing Cl current [IACh(Cl)]. The opener muscles differ from the ARC in that, in the openers, activation of IK(A) occurs approximately 9 mV more positive and there is much less IACh(Cl). In both muscles, IACh(cat) most likely serves to depolarize the muscle until ICa activates to supply Ca2+ for contraction, but further depolarization and spiking is opposed by coactivation of IK(A), IK(V), IK(Ca), and IACh(Cl). Thus the differences in IK(A) and IACh(Cl) may well be key factors that prevent spikes in the ARC but often allow them in the opener muscles. As in the ARC, the modulators enhance ICa and so potentiate contractions. They also activate a modulator-specific K current, which causes hyperpolarization and depression of contractions. Finally, in the opener muscles but not in the ARC, the modulators activate a depolarizing cationic current that may help phase-advance the contractions. Each modulator exerts these effects to different degrees and thus has a distinct effect on voltage and contraction size and shape. The overall effect then will depend on the specific combinations of modulators released in different behaviors. By understanding the modulation in the opener muscles, as well as in the ARC, we are now in a position to understand how the behavior of the two muscles is coordinated under a variety of circumstances.

4-(3-Butoxy-4-methoxybenzyl)-2-imidazolidinone↗
PubMed1999

Muscarine modulates Ca2+ channel currents in rat sensorimotor pyramidal cells via two distinct pathways.

We used the whole cell patch-clamp technique and single-cell reverse transcription-polymerase chain reaction (RT-PCR) to study the muscarinic receptor-mediated modulation of calcium channel currents in both acutely isolated and cultured pyramidal neurons from rat sensorimotor cortex. Single-cell RT-PCR profiling for muscarinic receptor mRNAs revealed the expression of m1, m2, m3, and m4 subtypes in these cells. Muscarine reversibly reduced Ca2+ currents in a dose-dependent manner. The modulation was blocked by the muscarinic antagonist atropine. When the internal recording solution included 10 mM ethylene glycol-bis(beta-aminoethyl ether)-N, N,N',N'-tetraacetic acid (EGTA) or 10 mM bis-(o-aminophenoxy)-N,N,N', N'-tetraacetic acid (BAPTA), the modulation was rapid (tauonset approximately 1.2 s). Under conditions where intracellular calcium levels were less controlled (0.0-0.1 mM BAPTA), a slowly developing component of the modulation also was observed (tauonset approximately 17 s). Both fast and slow components also were observed in recordings with 10 mM EGTA or 20 mM BAPTA when Ca2+ was added to elevate internal [Ca2+] ( approximately 150 nM). The fast component was due to a reduction in both N- and P-type calcium currents, whereas the slow component involved L-type current. N-ethylmaleimide blocked the fast component but not the slow component of the modulation. Preincubation of cultured neurons with pertussis toxin (PTX) also greatly reduced the fast portion of the modulation. These results suggest a role for both PTX-sensitive G proteins as well as PTX-insensitive G proteins in the muscarinic modulation. The fast component of the modulation was reversed by strong depolarization, whereas the slow component was not. Reblock of the calcium channels by G proteins (at -90 mV) occurred with a median tau of 68 ms. We conclude that activation of muscarinic receptors results in modulation of N- and P-type channels by a rapid, voltage-dependent pathway and of L-type current by a slow, voltage-independent pathway.

Animals↗
PubMed2002

Neural representations of sinusoidal amplitude and frequency modulations in the primary auditory cortex of awake primates.

We investigated neural coding of sinusoidally modulated tones (sAM and sFM) in the primary auditory cortex (A1) of awake marmoset monkeys, demonstrating that there are systematic cortical representations of embedded temporal features that are based on both average discharge rate and stimulus-synchronized discharge patterns. The rate-representation appears to be coded alongside the stimulus-synchronized discharges, such that the auditory cortex has access to both rate and temporal representations of the stimulus at high and low frequencies, respectively. Furthermore, we showed that individual auditory cortical neurons, as well as populations of neurons, have common features in their responses to both sAM and sFM stimuli. These results may explain the similarities in the perception of sAM and sFM stimuli as well as the different perceptual qualities effected by different modulation frequencies. The main findings include the following. 1) Responses of cortical neurons to sAM and sFM stimuli in awake marmosets were generally much stronger than responses to unmodulated tones. Some neurons responded to sAM or sFM stimuli but not to pure tones. 2) The discharge rate-based modulation transfer function typically had a band-pass shape and was centered at a preferred modulation frequency (rBMF). Population-averaged mean firing rate peaked at 16- to 32-Hz modulation frequency, indicating that the A1 was maximally excited by this frequency range of temporal modulations. 3) Only approximately 60% of recorded units showed statistically significant discharge synchrony to the modulation waveform of sAM or sFM stimuli. The discharge synchrony-based best modulation frequency (tBMF) was typically lower than the rBMF measured from the same neuron. The distribution of rBMF over the population of neurons was approximately one octave higher than the distribution of tBMF. 4) There was a high degree of similarity between cortical responses to sAM and sFM stimuli that was reflected in both discharge rate- or synchrony-based response measures. 5) Inhibition appeared to be a contributing factor in limiting responses at modulation frequencies above the rBMF of a neuron. And 6) neurons with shorter response latencies tended to have higher tBMF and maximum discharge synchrony frequency than those with longer response latencies. rBMF was not significantly correlated with the minimum response latency.

Acoustic Stimulation↗
PubMed1989

Evidence for heritability of non-modulating essential hypertension.

We have previously described a subset of subjects with essential hypertension who fail to appropriately modulate renal vascular and adrenal reactivity with changes in dietary sodium and in response to infused angiotensin II (Ang II). In this paper, we studied these responses in 13 unselected hypertensive subjects in whom the family history of hypertension had been carefully detailed. Nine of these 13 subjects had a positive family history (FH+) for hypertension and had significantly smaller decrements in renal blood flow with Ang II infusion than the four subjects who had a negative family history (FH-) (-84 +/- 16 ml/min/1.73 m2 for FH+ vs. -149 ml/min/1.73 m2 for FH-, p = 0.024). These FH+ subjects also showed smaller increases in renal blood flow with increases in dietary sodium than FH- subjects (7 +/- 10 ml/min/1.73 m2 vs. 72 +/- 24 ml/min/1.73 m2, respectively; p = 0.014). When classified as modulators or non-modulators by previously established criteria, all seven non-modulators were FH+, and seven of nine FH+ subjects were non-modulators. This association between non-modulation and family history of hypertension is significant (p = 0.021). To further clarify the association between non-modulation and family history of hypertension, we have studied the renal blood flow response to Ang II in 31 hypertensive siblings from 14 sibships. Twenty-five of these 31 subjects (81%) behaved as non-modulators (p = 0.008 compared with expected value in an unselected hypertensive population). Additionally, strong concordance of non-modulation between sibling pairs was observed (p = 0.004).(ABSTRACT TRUNCATED AT 250 WORDS)

Angiotensin II↗
PubMed1997

Age, gender, and non-modulation. A sexual dimorphism in essential hypertension.

The angiotensinogen gene is one of the very few related by linkage analysis to human hypertension, but the linkage has been consistently shown only among males. Moreover, polymorphisms in this gene predict an abnormal renal responsiveness to angiotensin II, a feature of non-modulation, but again, only among males. To pursue these related bridges between genetics and physiology, we evaluated the effects of sex on a second feature of non-modulation, the aldosterone response to infused angiotensin II during low sodium balance. We tested the resultant hypothesis-that non-modulation would be less frequent in women-by conducting identical protocols on 225 hypertensive inpatients (70 women, 155 men). Non-modulation was strikingly less frequent among women (26%; 95% confidence interval, 16% to 37%) than men (49%; 95% confidence interval, 40% to 57% (P = .001). We tested the hypothesis that sex steroids play a role by comparing young, premenopausal women (< 35 years) with women who were perimenopausal (45 to 55 years) and postmenopausal (> 55 years). Among the youngest women, the frequency of non-modulation was only 7%, significantly less than in young men (41%, P = .02). A steady increase in non-modulation frequency accompanied advancing age in women, reaching 47% in those older than 55 years, equal to the fraction of men affected. Age influenced non-modulation frequency in men far less. We conclude that a striking sex difference underlies the non-modulation phenotype and that female sex hormones may confer protection against a genotypic predisposition in women. This "override" of genotype, manifest by a very low frequency of non-modulation in young women, may participate in their known protection against cardiovascular disease.

Adolescent↗
PubMed1992

Effectiveness and replicability of modules for teaching social and instrumental skills to the severely mentally ill.

OBJECTIVE: This study evaluated the effectiveness and replicability of psychoeducational modules designed to improve the social and instrumental competencies of severely mentally ill patients. METHOD: Staff in seven facilities used the modules to teach 108 severely mentally ill patients. Staff received 2 days of formal training followed by periodic consultation. Each module's effectiveness was measured by a test of the patients' knowledge and performance of the skills taught in that module. Staff's adherence to the instructional techniques specified in the modules was measured by directly observing them and assessing the fidelity of their behaviors to those specified in the modules. RESULTS: The patients' skills significantly improved and were maintained during a 1-year follow-up, and staff accurately followed the modules with minimal consultation. CONCLUSIONS: These training modules are effective and replicable techniques for teaching social and instrumental skills to severely mentally ill patients. The modules can be easily disseminated to a variety of facilities and used as components in a comprehensive rehabilitation program.

Activities of Daily Living↗
PubMed2006

BLISS: binding site level identification of shared signal-modules in DNA regulatory sequences.

BACKGROUND: Regulatory modules are segments of the DNA that control particular aspects of gene expression. Their identification is therefore of great importance to the field of molecular genetics. Each module is composed of a distinct set of binding sites for specific transcription factors. Since experimental identification of regulatory modules is an arduous process, accurate computational techniques that supplement this process can be very beneficial. Functional modules are under selective pressure to be evolutionarily conserved. Most current approaches therefore attempt to detect conserved regulatory modules through similarity comparisons at the DNA sequence level. However, some regulatory modules, despite the conservation of their responsible binding sites, are embedded in sequences that have little overall similarity. RESULTS: In this study, we present a novel approach that detects conserved regulatory modules via comparisons at the binding site level. The technique compares the binding site profiles of orthologs and identifies those segments that have similar (not necessarily identical) profiles. The similarity measure is based on the inner product of transformed profiles, which takes into consideration the p values of binding sites as well as the potential shift of binding site positions. We tested this approach on simulated sequence pairs as well as real world examples. In both cases our technique was able to identify regulatory modules which could not to be identified using sequence-similarity based approaches such as rVista 2.0 and Blast. CONCLUSION: The results of our experiments demonstrate that, for sequences with little overall similarity at the DNA sequence level, it is still possible to identify conserved regulatory modules based solely on binding site profiles.

Animals↗
PubMed2004

Digital signal processing for step-scan phase and electrochemical potential double-modulation Fourier transform infrared spectrometry.

Step-scan double-modulation (phase and electrochemical potential) Fourier transform infrared (FT-IR) spectrometry provides both spectroscopic and dynamic information about faradaic reactions. Recently introduced digital signal processing (DSP) can be used, instead of two lock-in amplifiers, for the optical signal demodulation at two modulation frequencies. In order to establish the merits of double-modulation FT-IR spectrometry with DSP, spectro-electrochemical experiments are performed in the attenuated total reflection configuration and with the commonly used ferri/ferrocyanide redox couple. Because of a large potential drop associated with the uncompensated resistance, a satisfactory signal-to-noise ratio for the alternating current (ac) optical measurements is obtained only with the employment of positive feedback compensation. In this arrangement, the amplitude of electrochemical modulation is sufficiently large to convert a significant fraction of the reduced form to the oxidized form and back to the reduced form. Large amplitude ac voltammetry demonstrates that the phase of faradaic admittance at the formal potential is approximately 45 degrees at 2.00 Hz. In addition, these experiments allow for calculation of the interfacial ac potential. This variable is needed for the normalization of the in-phase and the quadrature spectra in order to overcome the problem associated with the iR(u) drop. Because of the integral relationship between the faradaic current and the electromodulation reflectance coefficient, the phases of electromodulation reflectance coefficient with respect to the interfacial ac potential are expected to be -45 degrees and 135 degrees for the reduced and oxidized forms, respectively. However, dynamic information from double-modulation FT-IR spectrometry is available only if demodulation at the electrochemical potential modulation frequency is performed with respect to a defined phase. Because of an undefined demodulation phase implemented in the current version of DSP software, step-scan double-modulation FT-IR spectrometry with DSP is suitable only to provide spectroscopic information. In order to overcome this limitation, the demodulation of the ac optical signal at the electrochemical modulation frequency must be synchronized in phase with the ac potential modulation applied to the electrochemical cell.

Journal Article↗
PubMed2006

Dispersal of boll weevils (Coleoptera: Curculionidae) from cotton modules before ginning.

We characterized the level of risk of boll weevil, Anthonomus grandis grandis Boheman, reintroduction to an eradication zone posed by dispersal from cotton modules during and after transport to the gin. Mark-release-recapture experiments in August and September in Texas indicated that most weevils disperse rapidly from the module surface, temperature permitting, unless confined under a module tarp, where most died. Nevertheless, 1-5% of released weevils were recovered alive after 24 h on the side and top surfaces of modules, representing potential dispersants. Mortality of boll weevils caged on the top surface of a module was 95-100% after 1-4 d when maximum air temperatures were > or = 33 degrees C and 72-100% when minimum temperatures were -7 degrees C or lower, but a few survived even after experiencing a minimum daily temperature of -12 degrees C. Under warm (daily maximum temperatures > or = 25 degrees C) and cold (daily minimum temperatures < or = 0 degrees C) weather conditions, survival was higher under the tarp than on the open surface of the module (20 versus 7% and 42 versus 26%, respectively), but mortality was 100% in both locations when temperatures reached 34 degrees C. Our results indicate that although the threat to an eradication zone posed by boll weevil dispersal from an infested module is very low under most environmental conditions, it is probably greatest when 1) a module is constructed and transported from an infested zone during weather too cool for flight, followed by warm weather favorable for flight at the gin yard; or 2) such a module is transported immediately after construction in moderate-to-warm weather.

Agriculture↗