Depth information in natural environments derived from optic flow by insect motion detection system: a model analysis

Knowing the depth structure of the environment is crucial for moving animals in many behavioral contexts, such as collision avoidance, targeting objects, or spatial navigation. An important source of depth information is motion parallax. This powerful cue is generated on the eyes during translatory self-motion with the retinal images of nearby objects moving faster than those of distant ones. To investigate how the visual motion pathway represents motion-based depth information we analyzed its responses to image sequences recorded in natural cluttered environments with a wide range of depth structures. The analysis was done on the basis of an experimentally validated model of the visual motion pathway of insects, with its core elements being correlation-type elementary motion detectors (EMDs). It is the key result of our analysis that the absolute EMD responses, i.e. the motion energy profile, represent the contrast-weighted nearness of environmental structures during translatory self-motion at a roughly constant velocity. In other words, the output of the EMD array highlights contours of nearby objects. This conclusion is largely independent of the scale over which EMDs are spatially pooled and was corroborated by scrutinizing the motion energy profile after eliminating the depth structure from the natural image sequences. Hence, the well-established dependence of correlation-type EMDs on both velocity and textural properties of motion stimuli appears to be advantageous for representing behaviorally relevant information about the environment in a computationally parsimonious way

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

<p>Abstract</p> <p>Background</p> <p>Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.</p> <p>Results</p> <p>OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions.</p> <p>Conclusion</p> <p>OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at <url>http://ontodas.nbn.ac.za</url></p

Temporal Statistics of Natural Image Sequences Generated by Movements with Insect Flight Characteristics

Schwegmann A, Lindemann JP, Egelhaaf M. Temporal Statistics of Natural Image Sequences Generated by Movements with Insect Flight Characteristics. PLoS ONE. 2014;9(10): e110386.Many flying insects, such as flies, wasps and bees, pursue a saccadic flight and gaze strategy. This behavioral strategy is thought to separate the translational and rotational components of self-motion and, thereby, to reduce the computational efforts to extract information about the environment from the retinal image flow. Because of the distinguishing dynamic features of this active flight and gaze strategy of insects, the present study analyzes systematically the spatiotemporal statistics of image sequences generated during saccades and intersaccadic intervals in cluttered natural environments. We show that, in general, rotational movements with saccade-like dynamics elicit fluctuations and overall changes in brightness, contrast and spatial frequency of up to two orders of magnitude larger than translational movements at velocities that are characteristic of insects. Distinct changes in image parameters during translations are only caused by nearby objects. Image analysis based on larger patches in the visual field reveals smaller fluctuations in brightness and spatial frequency composition compared to small patches. The temporal structure and extent of these changes in image parameters define the temporal constraints imposed on signal processing performed by the insect visual system under behavioral conditions in natural environments

Depth information in natural environments derived from optic flow by insect motion detection system: a model analysis

Schwegmann A, Lindemann JP, Egelhaaf M. Depth information in natural environments derived from optic flow by insect motion detection system: a model analysis. Frontiers in Computational Neuroscience. 2014;8:83.Knowing the depth structure of the environment is crucial for moving animals in many behavioral contexts, such as collision avoidance, targeting objects, or spatial navigation. An important source of depth information is motion parallax. This powerful cue is generated on the eyes during translatory self-motion with the retinal images of nearby objects moving faster than those of distant ones. To investigate how the visual motion pathway represents motion-based depth information we analyzed its responses to image sequences recorded in natural cluttered environments with a wide range of depth structures. The analysis was done on the basis of an experimentally validated model of the visual motion pathway of insects, with its core elements being correlation-type elementary motion detectors (EMDs). It is the key result of our analysis that the absolute EMD responses, i.e., the motion energy profile, represent the contrast-weighted nearness of environmental structures during translatory self-motion at a roughly constant velocity. In other words, the output of the EMD array highlights contours of nearby objects. This conclusion is largely independent of the scale over which EMDs are spatially pooled and was corroborated by scrutinizing the motion energy profile after eliminating the depth structure from the natural image sequences. Hence, the well-established dependence of correlation-type EMDs on both velocity and textural properties of motion stimuli appears to be advantageous for representing behaviorally relevant information about the environment in a computationally parsimonious way

New instruments of administrative procedure in Germany? : between acceptance and mediation

Disturbance of intestinal wound closure leads to insufficient anastomotic healing and is associated with considerable morbidity following colorectal resections. Matrix metalloproteinases (MMPs) play a crucial role in regulation of wound closure. Here fluorescence endoscopy was evaluated for assessment of MMP-2/-9 expression during failed intestinal anastomotic healing.Distal colonic anastomoses were performed as a model for disturbed healing in 36 Balb/c mice. Healing was evaluated endoscopically, macroscopically, and histologically after 1, 3 and 5 days. For detection of MMP-2/-9 expression fluorescence endoscopy (FE) was used following i.v.-administration of a Cy5.5-labeled MMP-2/-9 specific tracer. FE was complemented by quantification of the fluorescence signal using the MS-FX PRO Optical Imaging System. An overall leakage score was calculated and correlated with the results of FE.With increasing incidence of anastomotic leakage from POD1 (17%) to POD5 (83%) the uptake of the MMP tracer gradually increased (signal-to-noise ratio (SNR), POD1: 17.91 ± 1.251 vs. POD3: 30.56 ± 3.03 vs. POD5: 44.8 ± 4.473, P<0.0001). Mice with defective anastomotic healing showed significantly higher uptake compared to non-defective (SNR: 37.37± 3.63 vs. 26.16± 3.635, P = 0.0369). White light endoscopy and FE allowed evaluation of anastomotic healing and visualization of mucosal MMPs in vivo. Using FE based detection of MMPs in the anastomosis, an overall positive predictive value of 71.4% and negative predictive value of 66.6% was calculated for detection of anastomotic leakage.During disturbed anastomotic healing increased expression of MMP-2/-9 was observed in the anastomotic tissue. Fluorescence endoscopy for detection of MMP-2/-9 during the healing process might be a promising tool for early identification of anastomotic leakage

Determining crystal structures through crowdsourcing and coursework

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Camouflage evaluation by bio-inspired local conspicuity quantification

In this paper we will present a conspicuity quantification model based on anomaly detection. This model extracts numerous local image parameters, in first and higher order (transformation-based) statistics and calculates local conspicuity by a multiscale center-surround comparison, as a point in an image draws attention to it, if it significantly differs from its surroundings in one or more relevant parameters. This is also biologically substantiated, as many parts of the visual system calculate center-surround differences, for example in color or luminance. In our work we focused on biologically relevant parameters as the camouflage is targeted against human observers. In first order statistics we focused i.a. on local luminance, perceptual color difference in CIELAB color space, r.m.s. contrast and entropy. In the transformation-based higher order statistics we focused on spatial frequency distribution, power spectra, orientation bias and quefrency analysis via Fourier transformation and linear feature extraction via Radon Transformation. This, at first, enables the possibility to parametrize camouflage patterns and textures in a comprehensive way, offering a similarity rating of textures compared to a mean background, but in particular facilitates the calculation of conspicuity maps, in which eye-catching regions of images are highlighted. In this work we show that the linear combination of those conspicuity maps, gathered on different scales can provide a good value for local conspicuity and therefore directly acts as a useful quantification for camouflage, as drawing as little attention as possible to the camouflaged object quantified by a low conspicuity value results in a good camouflage rating

Consequences of self-motion on image statistics and depth perception in natural cluttered environments : a model analysis

Schwegmann A. Consequences of self-motion on image statistics and depth perception in natural cluttered environments : a model analysis. Bielefeld; 2014

Temporal statistics of natural image sequences generated by movements with insect flight characteristics.

Many flying insects, such as flies, wasps and bees, pursue a saccadic flight and gaze strategy. This behavioral strategy is thought to separate the translational and rotational components of self-motion and, thereby, to reduce the computational efforts to extract information about the environment from the retinal image flow. Because of the distinguishing dynamic features of this active flight and gaze strategy of insects, the present study analyzes systematically the spatiotemporal statistics of image sequences generated during saccades and intersaccadic intervals in cluttered natural environments. We show that, in general, rotational movements with saccade-like dynamics elicit fluctuations and overall changes in brightness, contrast and spatial frequency of up to two orders of magnitude larger than translational movements at velocities that are characteristic of insects. Distinct changes in image parameters during translations are only caused by nearby objects. Image analysis based on larger patches in the visual field reveals smaller fluctuations in brightness and spatial frequency composition compared to small patches. The temporal structure and extent of these changes in image parameters define the temporal constraints imposed on signal processing performed by the insect visual system under behavioral conditions in natural environments