Extraction of objects from structured backgrounds in the cat superior colliculus. Part II

Specific changes occur in the cells of the upper layers of the cat's superior colliculus when a two dimensional noise (background) is superimposed onto a deterministic signal (spot of light). Some of the measurements can be interpreted as meaning that some cells only react to certain relative movements of object (spot) and background (noise). The movement of the visual background is interpreted as environmental movement occurring due to the animal's own movement. The results of the measurements provide all the necessary presuppositions for a distinction between the animal's own velocity and that of the object (Part I). The experimental results can be interpreted with a model. The essential factor for the interpretation is the direction specific behavior of the cells which is bound up with an asymmetrical spatial coupling of the neurons with each other. The decisive advantage of asymmetrical systems for the pattern recognition of moving objects is that they can work without distortion and spatial displacement over large ranges of velocity (Part II).This research was supported by DFG Grant Se 251/7. Prof. Dr.-Ing. W. v. Seelen was in charge of the project     

Electrolocation and jamming avoidance in the mormyrid fishBrienomyrus

Brienomyrus niger fires its electric organ in short pulses of approximately 0.3 ms duration, at a rather irregular rate, which rapidly increases in novel situations. The animal electrolocates objects in its near field by evaluating electroreceptive feedback from its ownelectricorgandischarges (EODs). Electrolocation performance is measured by the critical distance at which an approaching nonconducting object of standard size and velocity is detected (Figs. 1, 3).Electrolocation performance is impaired when foreign pulses of sufficient intensity consistently coincide with the animal's own EODs, whereas noncoinciding pulses, even at intensities 10 times higher than that of the animal's own near field, have no effect. The animal needs at least 4 to 8 uncontaminated successive EODs to electrolocate optimally (Figs. 4, 5).     

Object detection in the fly during simulated translatory flight

Translatory movement of an animal in its environment induces optic flow that contains information about the three-dimensional layout of the surroundings: as a rule, images of objects that are closer to the animal move faster across the retina than those of more distant objects. Such relative motion cues are used by flies to detect objects in front of a structured background. We confronted flying flies, tethered to a torque meter, with front-to-back motion of patterns displayed on two CRT screens, thereby simulating translatory motion of the background as experienced by an animal during straight flight. The torque meter measured the instantaneous turning responses of the fly around its vertical body axis. During short time intervals, object motion was superimposed on background pattern motion. The average turning response towards such an object depends on both object and background velocity in a characteristic way: (1) in order to elicit significant responses object motion has to be faster than background motion; (2) background motion within a certain range of velocities improves object detection. These properties can be interpreted as adaptations to situations as they occur in natural free flight. We confirmed that the measured responses were mediated mainly by a control system specialized for the detection of objects rather than by the compensatory optomotor system responsible for course stabilization. Accepted: 20 March 1997     

Quantitative quality control in microarray image processing and data acquisition

A new integrated image analysis package with quantitative quality control schemes is described for cDNA microarray technology. The package employs an iterative algorithm that utilizes both intensity characteristics and spatial information of the spots on a microarray image for signal–background segmentation and defines five quality scores for each spot to record irregularities in spot intensity, size and background noise levels. A composite score q_com is defined based on these individual scores to give an overall assessment of spot quality. Using q_com we demonstrate that the inherent variability in intensity ratio measurements is closely correlated with spot quality, namely spots with higher quality give less variable measurements and vice versa. In addition, gauging data by q_com can improve data reliability dramatically and efficiently. We further show that the variability in ratio measurements drops exponentially with increasing q_com and, for the majority of spots at the high quality end, this improvement is mainly due to an improvement in correlation between the two dyes. Based on these studies, we discuss the potential of quantitative quality control for microarray data and the possibility of filtering and normalizing microarray data using a quality metrics-dependent scheme.     

The dilemma of the selfish herd: the search for a realistic movement rule

The selfish herd hypothesis predicts that aggregations form because individuals move toward one another to minimize their own predation risk. The "dilemma of the selfish herd" is that movement rules that are easy for individuals to follow, fail to produce true aggregations, while rules that produce aggregations require individual behavior so complex that one may doubt most animals can follow them. If natural selection at the individual level is responsible for herding behavior, a solution to the dilemma must exist. Using computer simulations, we examined four different movement rules. Relative predation risk was different for all four movement rules (p<0.05). We defined three criteria for measuring the quality of a movement rule. A good movement rule should (a) be statistically likely to benefit an individual that follows it, (b) be something we can imagine most animals are capable of following, and (c) result in a centrally compact flock. The local crowded horizon rule, which allowed individuals to take the positions of many flock-mates into account, but decreased the influence of flock-mates with distance, best satisfied these criteria. The local crowded horizon rule was very sensitive to the animal's perceptive ability. Therefore, the animal's ability to detect its neighbors is an important factor in the dynamics of group formation.     

Noise-dependent song amplitude regulation in a territorial songbird

Some animals that use sound to communicate compensate for interference from background noise by adjusting the amplitude of their vocalizations as environmental noise levels vary. Territorial songbirds may have evolved a different strategy, since they can be expected to benefit from maximizing the amplitude of their songs to defend territories and attract females. We tested this hypothesis with calibrated measurements of the song level of male nightingales, Luscinia megarhynchos. All birds increased the sound level of their songs in response to an increase in white noise broadcast to them. A second experiment revealed that noise in the spectral region of their own songs was most effective in inducing the birds to increase vocal intensity. These findings show that nightingales do not maximize song amplitude but regulate vocal intensity dependent on the level of masking noise. The adjustment of vocal amplitude may serve to maintain a specific signal-to-noise ratio that is favourable for signal production. Concurrently, increasing the intensity of songs can maintain a given active space for communication. Thus, vocal amplitude in a territorial songbird can be interpreted as a flexible trait, which is individually regulated according to ecological demands from signal transmission. Copyright 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.     

A novel strategy for microarray quality control using Bayesian networks

MOTIVATION: High-throughput microarray technologies enable measurements of the expression levels of thousands of genes in parallel. However, microarray printing, hybridization and washing may create substantial variability in the quality of the data. As erroneous measurements may have a drastic impact on the results by disturbing the normalization schemes and by introducing expression patterns that lead to incorrect conclusions, it is crucial to discard low quality observations in the early phases of a microarray experiment. A typical microarray experiment consists of tens of thousands of spots on a microarray, making manual extraction of poor quality spots impossible. Thus, there is a need for a reliable and general microarray spot quality control strategy. RESULTS: We suggest a novel strategy for spot quality control by using Bayesian networks, which contain many appealing properties in the spot quality control context. We illustrate how a non-linear least squares based Gaussian fitting procedure can be used in order to extract features for a spot on a microarray. The features we used in this study are: spot intensity, size of the spot, roundness of the spot, alignment error, background intensity, background noise, and bleeding. We conclude that Bayesian networks are a reliable and useful model for microarray spot quality assessment. SUPPLEMENTARY INFORMATION: http://sigwww.cs.tut.fi/TICSP/SpotQuality/.     

Tests of the limiting visual resolution of the DCMD system of the lubber grasshopper to rectangular gratings

Visual acuity measurements using the descending contralateral movement detector (DCMD) neuron in the lubber grasshopper, Romalea microptera, show responses to spatial angles as small as 0.3°. Moving, black-white striped objects were viewed on a rear-projection screen.Nonuniformity and spatial sub-harmonic measurements of the object patterns showed that any artifacts which were present were below the resolution limits of the human visual system (and presumably that of Romalea).Nonstationarity in the responses of the DCMD system can be categorized as long-term (sensitivity changes) and short term (habituation). A mathematical model for habituation is used to illustrate how confidence in responses may be lost due to the incorporation of too many samples of habituated data.     

In vivo micro particle image velocimetry measurements of blood-plasma in the embryonic avian heart

The measurement of blood-plasma velocity distributions with spatial and temporal resolution in vivo is inevitable for the determination of shear stress distributions in complex geometries at unsteady flow conditions like in the beating heart. A non-intrusive, whole-field velocity measurement technique is required that is capable of measuring instantaneous flow fields at sub-millimeter scales in highly unsteady flows. Micro particle image velocimetry (muPIV) meets these demands, but requires special consideration and methodologies in order to be utilized for in vivo studies in medical and biological research. We adapt muPIV to measure the blood-plasma velocity in the beating heart of a chicken embryo. In the current work, bio-inert, fluorescent liposomes with a nominal diameter of 400 nm are added to the flow as a tracer. Because of their small dimension and neutral buoyancy the liposomes closely follow the movement of the blood-plasma and allow the determination of the velocity gradient close to the wall. The measurements quantitatively resolve the velocity distribution in the developing ventricle and atrium of the embryo at nine different stages within the cardiac cycle. Up to 400 velocity vectors per measurement give detailed insight into the fluid dynamics of the primitive beating heart. A rapid peristaltic contraction accelerates the flow to peak velocities of 26 mm/s, with the velocity distribution showing a distinct asymmetrical profile in the highly curved section of the outflow tract. In relation to earlier published gene-expression experiments, the results underline the significance of fluid forces for embryonic cardiogenesis. In general, the measurements demonstrate that muPIV has the potential to develop into a general tool for instationary flow conditions in complex flow geometries encountered in cardiovascular research.     

家兔的开环及闭环视动震颤（OKN）研究

研究了家兔闭环及开环状态的ＯＫＮ反应。闭环时,ＯＫＮ眼动速度与刺激速度成正比,增益接近１。当固定受刺激眼形成开环状态时,ＯＫＮ眼动速度远大于刺激速度,增益可达１０２左右,说明ＯＫＮ系统是由运动跟踪的负反馈机制控制的;刺激范围缩小则眼动反应减弱,表明ＯＫＮ系统对运动信息具有空间总和作用;以视野中不同高度的局部刺激时,发现视网膜中央视带比周边部对ＯＫＮ刺激的敏感性高;单光点刺激视带中央可诱发出清楚的ＯＫＮ反应,这为临床上应用ＯＫＮ客观测定视网膜功能和运动感知提供了可能性。     

Hippocampus: memory, habit and voluntary movement

A general method for studying monkeys' memories is to teach the animals memory-dependent performance rules: for example, to choose, out of two visual stimuli, the one that flashed last time the animal saw it. One may thus assess the animal's memory for any arbitrarily chosen event such as flashing even if the event itself has no intrinsic importance for the animal. The method also allows assessment of an animal's memory of the animal's own previous behaviour. The use of these methods has revealed a simple generalization about the function of the hippocampus in memory: hippocampal lesions impair memory of the voluntary movement that a stimulus previously elicited, but leave intact memory for relations between environmental events other than voluntary movements. The impairment in memory for voluntary movements produces deficits in exploration and in habit formation.     

Synchronized firing among retinal ganglion cells signals motion reversal

We show that when a moving object suddenly reverses direction, there is a brief, synchronous burst of firing within a population of retinal ganglion cells. This burst can be driven by either the leading or trailing edge of the object. The latency is constant for movement at different speeds, objects of different size, and bright versus dark contrasts. The same ganglion cells that signal a motion reversal also respond to smooth motion. We show that the brain can build a pure reversal detector using only a linear filter that reads out synchrony from a group of ganglion cells. These results indicate that not only can the retina anticipate the location of a smoothly moving object, but that it can also signal violations in its own prediction. We show that the reversal response cannot be explained by models of the classical receptive field and suggest that nonlinear receptive field subunits may be responsible.     

Efficiency of a visual system under conditions of uncertainty of the appearance of a moving object

The effect of uncertainty of a moving object appearance in the noise field upon the coefficient efficiency, we studied. At short durations of presentation (40-80 msec) and high level of external noise, this effect was maximal: magnified 100 times. The efficiency coefficient dependence on the duration of a moving object presentation was shown to be characterized by two maximums. The position of minimum situated between these two maximums was found to be independent of either presence or absence of uncertainty of a number of parameters: such as initial position of the object the image, time of its appearance, noise level, velocity and direction of the movement, and has a latency approximately 120 sec. A functional model of the observed phenomena, has been proposed.     

The evolution of visual processing and the construction of seeing systems

This paper is concerned with the evolution of visual mechanisms and the possibility of copying their principles at different levels of sophistication. It is an old question how the complex interaction between eye and brain evolved when each needs the other as a test-bed for successive improvements. I propose that the primitive mechanism for the separation of stationary objects relies on their relative movement against a background, normally caused by the animal's own movement. Apparently insects and many lower animals use little more than this for negotiating through a three-dimensional world, making adequate responses to individual objects which they 'see' without a cortical system or even without a large brain. In the development of higher animals such as birds or man, additional circuits store memories of the forms of objects that have been frequently inspected from all angles or handled. Simple visual systems, however, are tuned to a feature of the world by which objects separate themselves by movement relative to the eye. In making simple artificial visual systems which 'see', as distinct from merely projecting the image, it is more hopeful to copy the 'ambient' vision of lower animals than the cortical systems of birds or mammals.     

Bacterium in a box: sensing of quorum and environment by the <Emphasis Type="BoldItalic">LuxI/LuxR</Emphasis> gene regulatory circuit

The chemical signaling mechanism known as “bacterial quorum sensing” (QS) is normally interpreted as allowing bacteria to detect their own population density, in order to coordinate gene expression across a colony. However, the release of the chemical signal can also be interpreted as a means for one or a few cells to probe the local physical properties of their microenvironment. We have studied the behavior of the LuxI/LuxR QS circuit of Vibrio fischeri in tightly confining environments where individual cells detect their own released signals. We find that the lux genes become activated in these environments, although the activation onset time shows substantial cell-to-cell variability and little sensitivity to the confining volume. Our data suggest that noise in gene expression could significantly impact the utility of LuxI/LuxR as a probe of the local physical environment.     

Detour behavior in the Quokka (Setonix brachyurus)

Four quokkas (Setonix brachyurus) were tested in their natural environment for the ability to progress around a barrier to a desired goal object (food). Symmetrical and asymmetrical barriers were used with different lengths of side arm. Three quokkas showed significant tendencies to progress either left or right around the barrier, though this laterality declined as the length of the side arm of the barrier was extended. One quokka showed no behavioral laterality and this animal was also the only one to show spatial reasoning (spontaneous selection of the shorter route on first presentation of the asymmetrical barrier) as opposed to spatial learning (progressive improvement in choice of the shorter route with repeated experience).     

Figure-ground discrimination by relative movement in the visual system of the fly

The visual system of the fly performs various computations on photoreceptor outputs. The detection and measurement of movement is based on simple nonlinear multiplication-like interactions between adjacent pairs and groups of photoreceptors. The position of a small contrasted object against a uniform background is measured, at least in part, by (formally) 1-input nonlinear flicker detectors. A fly can also detect and discriminate a figure that moves relative to a ground texture. This computation of relative movement relies on a more complex algorithm, one which detects discontinuities in the movement field. The experiments described in this paper indicate that the outputs of neighbouring movement detectors interact in a multiplication-like fashion and then in turn inhibit locally the flicker detectors. The following main characteristic properties (partly a direct consequence of the algorithm's structure) have been established experimentally: a) Coherent motion of figure and ground inhibit the position detectors whereas incoherent motion fails to produce inhibition near the edges of the moving figure (provided the textures of figure and ground are similar). b) The movement detectors underlying this particular computation are direction-insensitive at input frequencies (at the photoreceptor level) above 2.3 Hz. They become increasingly direction-sensitive for lower input frequencies. c) At higher input frequencies the fly cannot discriminate an object against a texture oscillating at the same frequency and amplitude at 0° and 180° phase, whereas 90° or 270° phase shift between figure and ground oscillations yields maximum discrimination. d) Under conditions of coherent movement, strong spatial incoherence is detected by the same mechanism. The algorithm underlying the relative movement computation is further discussed as an example of a coherence measuring process, operating on the outputs of an array of movement detectors. Possible neural correlates are also mentioned.     

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements

Background  

High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e.g. repetitive regions or non-specific antibody interactions. The noise will appear in the form of a background distribution of reads that must be taken into account in the downstream analysis, for example when detecting enriched regions (peak-calling). Several reported peak-callers can take experimental measurements of background tag distribution into account when analysing a data set. Unfortunately, the background is only used to adjust peak calling and not as a pre-processing step that aims at discerning the signal from the background noise. A normalization procedure that extracts the signal of interest would be of universal use when investigating genomic patterns.     

White noise analysis of graded response in a wind-sensitive,nonspiking interneuron of the cockroach

1. A novel approach using a Gaussian white noise as stimulus is described which allowed quantitative analysis of neuronal responses in the cercal system of the cockroach, Periplaneta americana. Cerci were stimulated by air displacement which was modulated by a sinusoidal and a white noise signal. During the stimulation, intracellular recordings were made from a uniquely identifiable, nonspiking, local interneuron which locates within the terminal abdominal ganglion. The white noise stimulation was cross-correlated with the evoked response to compute first- and second-order kernels that could define the cell's response dynamics. 2. The interneuron, cell 101, has an exceptionally large transverse neurite that connects two asymmetrical dendritic arborizations located on both sides of the ganglion. 3. The first-order Wiener kernels in cell 101 were biphasic (differentiating). The waveforms of the kernels produced by the ipsilateral and contralateral stimulations were roughly mirror images of each other: the kernels produced by wind stimuli on the side ipsilateral to the cell body of the interneuron are initially depolarized and then hyperpolarized, whereas those on the other side are initially hyperpolarized. The polarity reversal occurred along the midline of the animal's body, and no well-defined kernel was produced by a stimulus directed head on or from the tail. 4. Mean square error (MSE) between the actual response and the model prediction suggests that the linear component in cell 101 comprises half of the cell's total response (MSEs for the linear models were about 50% at preferred directions), whereas the second-order, non-linear component is insignificant. The linear component of the wind-evoked response was bandpass with the preferred frequency of 70-90 Hz. 5. Accounting for a noise, we reasonably assumed that at high frequencies the graded response in cell 101 is linearly related to a modulation of the air displacement and sensitive to the rate of change of the signal (i.e., wind velocity) and the direction of its source. It is suggested that the dynamics of the first-order kernel simply reflect the dynamics of sensory receptors that respond linearly to wind stimulation.