Implementation of a field programmable gate array based transcranial Doppler ultrasound system using pulse compression techniques

A field programmable gate array (FPGA) based hardware platform that is used to implement a digital, multi-gate pulsed Doppler ultrasound system for transcranial Doppler (TCD) use is described. The Doppler audio signal is extracted from the digitised radio-frequency signal by matched filtering and suitable sampling. The system was configured to acquire Doppler signals from 16 depth locations and to display Doppler signal power versus depth as well as a sonogram from a user specified depth. The signal-to-noise performance of the system was comparable with that of a commercially available TCD unit for equivalent pulse repetition frequency and sample volume settings.The flexibility of the platform was used to demonstrate the feasibility of using coded transducer excitation and pulse compression techniques to improve axial resolution compared to a non-coded implementation. The axial resolution improvement was demonstrated using a flow phantom and measured using a vibrating wire phantom. The measured resolutions were 9.1 and 2.4 mm for the conventional and coded implementations, respectively. The reduction in signal-to-noise ratio of approximately 5 dB associated with the configuration using coded excitation was attributable to the frequency response characteristics of the transducer rather than the processing technique used. This work demonstrates both the flexibility associated with an FPGA implementation of a Doppler ultrasound system and the potential for coded excitation to improve axial resolution in TCD systems.     

普氏蹄蝠(Hipposideros pratti)回声定位声波、形态及捕食策略

研究了普氏蹄蝠（Hipposideros pratti)不同状态（飞行,悬挂）下的回声定位声波特征,形态特征和生态特征（捕食策略,捕食地和食物类型）。结果表明,普氏蹄蝠的回声定位声波为CF－FM型,在不同状态下,主频率有一定的差异,飞行状态的主频率略低于悬挂状态,表明普氏蹄蝠是利用多谱勒补偿效应来适应飞行速度引起的主频率变化,以进行准确的定位和有效的捕食;同时飞行状态下声脉冲时间,声脉冲间隔时间及FM带宽略低于悬挂状态,而声脉冲重复率和能率环略主于悬挂状态,表明普氏蹄蝠在不同状态下利用不同特征的声波进行捕食,由回声定位声波推断和野外观察可知,普氏蹄蝠可能在树冠周围以盘旋方式（在昆虫高峰期）或以捕蝇器式（在昆虫高峰期这后）捕食中等偏大的振翅昆虫（如甲虫）。     

Responses of auditory brainstem neurons in the grassfrog to clicks

Single unit recordings were made in the dorsal medullary nucleus and in the torus semicircularis of the immobilized grassfrog. The natural calls have a periodic pulsatile structure. To investigate the coding of pulse repetition rate periodic click trains with varying pulse repetition rate and an ensemble of clicks distributed randomly in time were used as stimuli. In the dorsal medullary nucleus strong time-locking to clicks was found. Most units showed an activation followed by suppression response. Some units showed a preference for pulse repetition rates matching their low-frequency sensitivity. In the torus semicircularis part of the units showed responses similar to dorsal medullary nucleus units. Other response types were activation irrespective of pulse repetition rate, and suppression followed by activation. The responses to the two stimulus ensembles were more compatible in the dorsal medullary nucleus than in the torus semicircularis.     

The resolution of the ultrasound pulsed Doppler for blood velocity measurements

Pulsed ultrasound Doppler velocity meters (PUDVM) permit noninvasive blood velocity measurements. The emitted ultrasound beam characteristics primarily determine the resolution of the instrument when recording velocity profiles. The sample volume, the small region over which velocity information data are detected, was found to be > 2·3 mm³ depending on the transducer disk dia., distance in front of the disk, sampling time increment, and pulse length. The shape of the sample volume approximates a cylinder in the near field and a frustrum of a cone in the far field. The end surfaces of the sample volume were affected by the emitted pulse shape. Ultrasonic beam cross-sections were found to be smaller than predicted by theory due to the finite threshold levels of the PUDVM. The variation of the sample volume with range was illustrated by steady laminar flow velocity profile measurements in rigid tubes. The accuracy of velocity measurements was within 5 per cent with slightly larger deviations occurring near the walls due to the finite sample volume.     

普氏蹄蝠(Hipposideros pratti)回声定位声波、形态及捕食策略

研究了普氏蹄蝠(Hipposideros pratti)不同状态(飞行、悬挂)下的回声定位声波特征、形态特征和生态特征(捕食策略、捕食地和食物类型).结果表明,普氏蹄蝠的回声定位声波为CFFM型,在不同状态下,主频率有一定的差异,飞行状态的主频率略低于悬挂状态,表明普氏蹄蝠是利用多谱勒补偿效应来适应飞行速度引起的主频率变化,以进行准确的定位和有效的捕食;同时飞行状态下声脉冲时间、声脉冲间隔时间及FM带宽略低于悬挂状态,而声脉冲重复率和能率环略高于悬挂状态,表明普氏蹄蝠在不同状态下利用不同特征的声波进行捕食.由回声定位声波推断和野外观察可知,普氏蹄蝠可能在树冠周围以盘旋方式(在昆虫高峰期)或以捕蝇器式(在昆虫高峰期之后)捕食中等偏大的振翅昆虫(如甲虫).     

The adaptive value of increasing pulse repetition rate during hunting by echolocating bats

During hunting, bats of suborder Microchiropetra emit intense ultrasonic pulses and analyze the weak returning echoes with their highly developed auditory system to extract the information about insects or obstacles. These bats progressively shorten the duration, lower the frequency, decrease the intensity and increase the repetition rate of emitted pulses as they search, approach, and finally intercept insects or negotiate obstacles. This dynamic variation in multiple parameters of emitted pulses predicts that analysis of an echo parameter by the bat would be inevitably affected by other co-varying echo parameters. The progressive increase in the pulse repetition rate throughout the entire course of hunting would presumably enable the bat to extract maximal information from the increasing number of echoes about the rapid changes in the target or obstacle position for successful hunting. However, the increase in pulse repetition rate may make it difficult to produce intense short pulse at high repetition rate at the end of long-held breath. The increase in pulse repetition rate may also make it difficult to produce high frequency pulse due to the inability of the bat laryngeal muscles to reach its full extent of each contraction and relaxation cycle at a high repetition rate. In addition, the increase in pulse repetition rate increases the minimum threshold (i.e. decrease auditory sensitivity) and the response latency of auditory neurons. In spite of these seemingly physiological disadvantages in pulse emission and auditory sensitivity, these bats do progressively increase pulse repetition rate throughout a target approaching sequence. Then, what is the adaptive value of increasing pulse repetition rate during echolocation? What are the underlying mechanisms for obtaining maximal information about the target features during increasing pulse repetition rate? This article reviews the electrophysiological studies of the effect of pulse repetition rate on multiple-parametric selectivity of neurons in the central nucleus of the inferior colliculus of the big brown bat, Eptesicus fuscus using single repetitive sound pulses and temporally patterned trains of sound pulses. These studies show that increasing pulse repetition rate improves multiple-parametric selectivity of inferior collicular neurons. Conceivably, this improvement of multiple-parametric selectivity of collicular neurons with increasing pulse repetition rate may serve as the underlying mechanisms for obtaining maximal information about the prey features for successful hunting by bats.     

Knowledge-based nonuniform sampling in multidimensional NMR

The full resolution afforded by high-field magnets is rarely realized in the indirect dimensions of multidimensional NMR experiments because of the time cost of uniformly sampling to long evolution times. Emerging methods utilizing nonuniform sampling (NUS) enable high resolution along indirect dimensions by sampling long evolution times without sampling at every multiple of the Nyquist sampling interval. While the earliest NUS approaches matched the decay of sampling density to the decay of the signal envelope, recent approaches based on coupled evolution times attempt to optimize sampling by choosing projection angles that increase the likelihood of resolving closely-spaced resonances. These approaches employ knowledge about chemical shifts to predict optimal projection angles, whereas prior applications of tailored sampling employed only knowledge of the decay rate. In this work we adapt the matched filter approach as a general strategy for knowledge-based nonuniform sampling that can exploit prior knowledge about chemical shifts and is not restricted to sampling projections. Based on several measures of performance, we find that exponentially weighted random sampling (envelope matched sampling) performs better than shift-based sampling (beat matched sampling). While shift-based sampling can yield small advantages in sensitivity, the gains are generally outweighed by diminished robustness. Our observation that more robust sampling schemes are only slightly less sensitive than schemes highly optimized using prior knowledge about chemical shifts has broad implications for any multidimensional NMR study employing NUS. The results derived from simulated data are demonstrated with a sample application to PfPMT, the phosphoethanolamine methyltransferase of the human malaria parasite Plasmodium falciparum.     

A three-dimensional computational simulation of some sources of measurement artifact in microvascular pulsed ultrasound Doppler velocimetry

Recent applications of 20 MHz pulsed ultrasound Doppler velocimetry (PUDVM) in microsurgical research have necessarily employed piezoelectric crystals whose diameter is not negligible compared to the lumen size (1-2 mm) of many vessels of interest. A three-dimensional numerical model was developed to explore relationships between actual and detected flow field parameters, for (steady) Poiseuille flow, when appreciable velocity gradients exist within the PUDVM sample volume. Validation studies showed that highly accurate velocity profiles could be obtained in the limiting case of a very small sample volume (0.1 mm radius), but that for currently employed crystals (approximately equal to 0.5 mm radius) there was appreciable underestimation of the centersteam velocity, and appreciable overestimation of the flow stream diameter. Errors in perceived velocity and flow rate were found to be relatively insensitive to perturbations in the sample volume thickness, in the size of the sampling range increment, or in the angle of insonation beam divergence. By contrast, these apparent flow parameters were found to be very sensitive to perturbations of sample volume diameter or of the Doppler angle. Small variations in the degree of partial sample volume overlap of the flowstream periphery were shown to be capable of causing large fluctuations in apparent flow stream diameter.     

Ensemble modeling of metabolic networks

Complete modeling of metabolic networks is desirable, but it is difficult to accomplish because of the lack of kinetics. As a step toward this goal, we have developed an approach to build an ensemble of dynamic models that reach the same steady state. The models in the ensemble are based on the same mechanistic framework at the elementary reaction level, including known regulations, and span the space of all kinetics allowable by thermodynamics. This ensemble allows for the examination of possible phenotypes of the network upon perturbations, such as changes in enzyme expression levels. The size of the ensemble is reduced by acquiring data for such perturbation phenotypes. If the mechanistic framework is approximately accurate, the ensemble converges to a smaller set of models and becomes more predictive. This approach bypasses the need for detailed characterization of kinetic parameters and arrives at a set of models that describes relevant phenotypes upon enzyme perturbations.     

The influence of stimulus duration on the delay tuning of cortical neurons in the FM bat,Myotis lucifugus

1. Echolocating bats use echo delay as the primary cue to determine target distance. During target-directed flight, the emitted pulses increase in repetition rate and shorten in duration as distance decreases. To determine how these parameters affect the delay tuning of neurons in the auditory cortex of the awake bat, Myotis lucifugus, we examined the responses of 104 delay-sensitive neurons as the pulse repetition rate (PRR) and duration were independently varied. Stimulus duration of 4, 2 and 1 ms and PRR of 5-100/s were used for both the pulse and echo to determine delay sensitivity. These parameter ranges span those used during the search, approach, and the initial terminal phases of echolocation. 2. As the stimulus duration was shortened, the range of PRRs for delay sensitivity was extended to higher rates in 41% of the neurons, narrowed or disappeared in 40%, and remained unchanged in 4%. The remaining 15% were not categorized since it was not possible to determine a trend in which the range of delay-sensitive PRRs changed with stimulus duration. 3. Three types of tracking neurons (i.e., neurons that change their best delay during target-directed flight) were found. For the first type, the best delay (BD) shortened with shorter stimulus duration, for the second type, BD shortened with both shorter stimulus durations and higher PRRs, and for the third type, BD shortened with higher PRRs. 4. These results suggest that the stimulus parameters of sonar emission influence delay tuning and hence processing by cortical neurons in FM bats.     

Mathematische Auswertung von Daten für das Wachstum von Heringen der Nordsee

The parameters of the reciprocal function (“Reziprokfunktion”) for the growth of herrings(Clupea harengus) are calculated from older and more recent measurements. The logarithmic expression of the proposed reciprocal function is as follows: \(\log y_x = \log y_{max} - \frac{1}{{\chi + \xi }}\log N\) . Values less than 1 are found for the additive age (ξ). In further calculations 0.4 is used as the estimated mean value. Measurements made before the second world war yield ca. 30 cm for the maximum value (L_max). After this period the maximum values increase to ca. 34 cm. The Scandinavian and Atlantic herrings differ from North Sea herrings by higher maximum values. The values for the constant of velocity (log N) may be different for identical ξ and Y_max values. The velocity constant determines the position of the inflection point of the growth curve. The dimension, which is only dependent on the maximum value, is at the inflection point: \(\frac{{Y_{max} }}{{7,389}}\) . From the results ofSchumacher (1967) on the growth of 3 herring populations from the North Sea it was calculated that the values for the constant of velocity rise from northern to southern areas. A low value for the constant of velocity marks an early inflection point and a high velocity of growth before this point and vice versa. The growth of the 3 populations tends to almost the same maximum value; consequently, a high velocity before the inflection point is compensated by a lower velocity after this point and vice versa. The maximum velocity of linear growth at the point of inflection is given by the expression \(\frac{{Y_{max} }}{{4,25 \cdot \log N}}\) . This expression may possibly be a useful device for quantitative comparisons of growth processes.     

Selecting High Quality Protein Structures from Diverse Conformational Ensembles

Protein structure prediction encompasses two major challenges: 1), the generation of a large ensemble of high resolution structures for a given amino-acid sequence; and 2), the identification of the structure closest to the native structure for a blind prediction. In this article, we address the second challenge, by proposing what is, to our knowledge, a novel iterative traveling-salesman problem-based clustering method to identify the structures of a protein, in a given ensemble, which are closest to the native structure. The method consists of an iterative procedure, which aims at eliminating clusters of structures at each iteration, which are unlikely to be of similar fold to the native, based on a statistical analysis of cluster density and average spherical radius. The method, denoted as ICON, has been tested on four data sets: 1), 1400 proteins with high resolution decoys; 2), medium-to-low resolution decoys from Decoys ‘R’ Us; 3), medium-to-low resolution decoys from the first-principles approach, ASTRO-FOLD; and 4), selected targets from CASP8. The extensive tests demonstrate that ICON can identify high-quality structures in each ensemble, regardless of the resolution of conformers. In a total of 1454 proteins, with an average of 1051 conformers per protein, the conformers selected by ICON are, on an average, in the top 3.5% of the conformers in the ensemble.     

The role of GABAergic inhibition in shaping directional selectivity of bat inferior collicular neurons determined with temporally patterned pulse trains

This study examined the role of GABAergic inhibition in shaping directional selectivity of neurons in the inferior colliculus of the big brown bat, Eptesicus fuscus. When determined with temporally patterned pulse trains at different pulse repetition rates, 93 inferior colliculus neurons displayed three types of directional selectivity curves. A directionally selective curve always showed a maximum to a certain azimuthal angle (the best angle). A hemifield curve showed a maximum to a range of contralateral azimuthal angles. A non-directional curve did not show a maximum to any particular azimuthal angles. Directional selectivity curves of 42% neurons changed from hemifield or non-directional to directionally selective and the best angles of 16-21% neurons shifted toward the midline with increasing pulse repetition rate of pulse trains. Directional selectivity curves of most (74%) neurons that discharged impulses to each pulse of a pulse train also became sharper with increasing pulse repetition rate of pulse trains. Bicuculline application produced more pronounced broadening of directional selective curves of inferior colliculus neurons at higher than at lower pulse repetition rates. As a result, pulse repetition rate-dependent directional selectivity of inferior colliculus neurons was abolished. Possible mechanisms and biological significance of these findings are discussed.     

Electrohydrodynamic effect resulting from high-frequency barrier discharge in gas

The formation of an electrohydrodynamic flow in atmospheric air by using a high-frequency barrier discharge distributed over the dielectric surface is investigated. The influence of variations in parameters of a fully solid-state pulse generator (with a peak voltage of 0–12 kV, a tunable repetition rate of 10–25 kHz, and a pulse duration of 7 μs) on the current of plasma ion emitter and velocity characteristics of airflow is considered.     

How Fast Is Your Body Motion? Determining a Sufficient Frame Rate for an Optical Motion Tracking System Using Passive Markers

This paper addresses how to determine a sufficient frame (sampling) rate for an optical motion tracking system using passive reflective markers. When using passive markers for the optical motion tracking, avoiding identity confusion between the markers becomes a problem as the speed of motion increases, necessitating a higher frame rate to avoid a failure of the motion tracking caused by marker confusions and/or dropouts. Initially, one might believe that the Nyquist-Shannon sampling rate estimated from the assumed maximal temporal variation of a motion (i.e. a sampling rate at least twice that of the maximum motion frequency) could be the complete solution to the problem. However, this paper shows that also the spatial distance between the markers should be taken into account in determining the suitable frame rate of an optical motion tracking with passive markers. In this paper, a frame rate criterion for the optical tracking using passive markers is theoretically derived and also experimentally verified using a high-quality optical motion tracking system. Both the theoretical and the experimental results showed that the minimum frame rate is proportional to the ratio between the maximum speed of the motion and the minimum spacing between markers, and may also be predicted precisely if the proportional constant is known in advance. The inverse of the proportional constant is here defined as the tracking efficiency constant and it can be easily determined with some test measurements. Moreover, this newly defined constant can provide a new way of evaluating the tracking algorithm performance of an optical tracking system.     

Triple Quantum Decoherence under Multiple Refocusing: Slow Correlated Chemical Shift Modulations of C′ and N Nuclei in Proteins

A new experiment allows the identification of residues that feature slow conformational exchange in macromolecules. Rotations about dihedral angles that are slower than the global correlation time tau(c) cause a modulation of the isotropic chemical shifts of the nuclei. If these fluctuations are correlated they induce a differential line broadening between three-spin single-quantum and triple-quantum coherences involving three nuclei such as the carbonyl C', the neighbouring amide nitrogen N and the amide proton H(N) belonging to a pair of consecutive amino acids. A cross-correlated relaxation rate R (CS/CS)(C'N) can be determined that corresponds to the sum of the isotropic and anisotropic contributions to the chemical shift modulations of the carbonyl carbon and nitrogen nuclei. Only the isotropic contributions depend on the pulse repetition rate of a multiple-refocusing sequence. An attenuation of the relaxation rate with increasing pulse repetition rate can therefore be attributed to slow motions. The asparagine N25 residue of ubiquitin, located in the first alpha-helix, is shown to feature significant slow conformational exchange.     

ANALYSIS OF SOUNDS PRODUCED BY MALE PADOGOBIUS MARTENSI (PISCES,GOBIIDAE) AND FACTORS AFFECTING THEIR STRUCTURAL PROPERTIES

ABSTRACT

In this paper a detailed analysis of the physical structure of sounds produced by male Padogobius martensi is reported. Sound production occurs during courtship and inter-male agonistic encounters. Both aggressive and courtship calls are made up of rapidly repeated pulses, with a pulse repetition rate decreasing through the course of the emission. By means of computerized analysis, the pulse repetition rate, its modulation and sound duration were determined. The water temperature was found to exert a marked and significant effect on the above parameters. In particular, the temperature directly affects the pulse rate and its decrease through the course of the emission (i.e. frequency modulation) and inversely affects sound duration. By contrast, size of the calling animal does not significantly influence the sound parameters considered. Aggressive sounds last longer and have a lower pulse repetition rate than the courtship sounds. Moreover, aggressive sounds appear more variable than the courtship ones as far as pulse rate and duration are concerned.     

Are Tropical Highland Frog Calls Cold–adapted? The Case of the Andean Frog Hyla labialis1

Across a wide range of temperatures established in the laboratory, we tape–recorded the advertisement calls of 76 freshly caught Hyla labialis males from three elevationally separated populations in the Eastern Andes of Colombia. Each male was tested once at a single temperature and returned to his capture site after measurement of his snout–vent length. We measured and averaged three characteristics of five to ten successive calls for each individual: number of pulses per call, pulse repetition rate, and call duration. We found that calling activity occurred within temperature ranges that overlapped among frogs from different elevations, but widened and shifted downward with increasing altitude of origin. Males from all sites called at temperatures higher, but not lower, than those naturally occurring during their nightly activity period. No decline in vocal performance was apparent when frogs extended their calling activity into the range of high temperatures selected for basking. Both snout–vent length and temperature affected pulse repetition rate and call duration, while the number of pulses per call was temperature–independent. Compared to the smaller males from lower elevations, the larger, high–mountain males had calls with significandy more pulses, a lower pulse repetition rate, and longer duration. Within each population, rising temperatures caused pulse repetition rate to increase and call duration to decrease significantly, whereas the number of pulses per call remained unchanged. Pulse repetition rate of highland males was the factor least affected by temperature, and it was less sensitive to night temperatures than to day temperatures. This, together with their capacity to call at low temperatures, suggests that highland frog calls are cold adapted.     

Temporal estimates of effective population size in species with overlapping generations

The standard temporal method for estimating effective population size (N(e)) assumes that generations are discrete, but it is routinely applied to species with overlapping generations. We evaluated bias in the estimates N(e) caused by violation of this assumption, using simulated data for three model species: humans (type I survival), sparrow (type II), and barnacle (type III). We verify a previous proposal by Felsenstein that weighting individuals by reproductive value is the correct way to calculate parametric population allele frequencies, in which case the rate of change in age-structured populations conforms to that predicted by discrete-generation models. When the standard temporal method is applied to age-structured species, typical sampling regimes (sampling only newborns or adults; randomly sampling the entire population) do not yield properly weighted allele frequencies and result in biased N(e). The direction and magnitude of the bias are shown to depend on the sampling method and the species' life history. Results for populations that grow (or decline) at a constant rate paralleled those for populations of constant size. If sufficient demographic data are available and certain sampling restrictions are met, the Jorde-Ryman modification of the temporal method can be applied to any species with overlapping generations. Alternatively, spacing the temporal samples many generations apart maximizes the drift signal compared to sampling biases associated with age structure.