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92 Publications

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    12/29/06 | The virtual insect brain protocol: creating and comparing standardized neuroanatomy.
    Jenett A, Schindelin JE, Heisenberg M
    BMC Bioinformatics. 2006 Dec 29;7:544. doi: 10.1186/1471-2105-7-544

    In the fly Drosophila melanogaster, new genetic, physiological, molecular and behavioral techniques for the functional analysis of the brain are rapidly accumulating. These diverse investigations on the function of the insect brain use gene expression patterns that can be visualized and provide the means for manipulating groups of neurons as a common ground. To take advantage of these patterns one needs to know their typical anatomy.

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    12/01/06 | A double-switch system regulates male courtship behavior in male and female Drosophila melanogaster.
    Shirangi TR, Taylor BJ, McKeown M
    Nature Genetics. 2006 Dec;38(12):1435-9. doi: 10.1038/ng1908

    Current models describe male-specific fruitless (fruM) as a genetic ’switch’ regulating sexual behavior in Drosophila melanogaster, and they postulate that female (F) and male (M) doublesex (dsx) products control body sexual morphology. In contradiction to this simple model, we show that dsx, as well as fruM and non-sex-specific retained (retn), affect both male and female sexual behaviors. In females, both retn and dsxF contribute to female receptivity, and both genes act to repress male-like courtship activity in the presence or absence of fruM. In males, consistent with the opposing functions of dsxM and dsxF, dsxM acts as a positive factor for male courtship. retn also acts counter to fruM in the development of the male-specific muscle of Lawrence. Molecularly, retn seems to regulate sexual behavior via a previously described complex that represses zerknullt. Thus, we show that fru and dsx together act as a ’switch’ system regulating behavior in the context of other developmental genes, such as retn.

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    12/01/06 | A new role for microRNA pathways: modulation of degeneration induced by pathogenic human disease proteins.
    Bilen J, Liu N, Bonini NM
    Cell Cycle . 2006 Dec;5(24):2835-8

    MicroRNAs (miRNAs) are small noncoding RNAs that regulate the expression of target transcript mRNAs. Many miRNAs have been defined, however their roles and the processes influenced by miRNA pathways are still being elucidated. A role for miRNAs in development and cancer has been described. We recently isolated the miRNA bantam (ban) in a genetic screen for modulators of pathogenicity of a human neurodegenerative disease model in Drosophila. These studies showed that upregulation of ban mitigates degeneration induced by the pathogenic polyglutamine (polyQ) protein Ataxin-3, which is mutated in the human polyglutamine disease spinocerebellar ataxia type 3 (SCA3). To address the broader role for miRNAs in neuroprotection, we also showed that loss of all miRNAs, by dicer mutation, dramatically enhances pathogenic polyQ protein toxicity in flies and in human HeLa cells. These studies suggest that miRNAs may be important for neuronal survival in the context of human neurodegenerative disease. These studies provide the foundation to define the miRNAs involved in neurodegenerative disease, and the biological pathways affected.

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    Egnor Lab
    12/01/06 | Noise-induced vocal modulation in cotton-top tamarins (Saguinus oedipus).
    Egnor SE, Hauser MD
    American Journal of Primatology. 2006 Dec;68(12):1183-90. doi: 10.1002/ajp.20317

    The Lombard effect-an increase in vocalization amplitude in response to an increase in background noise-is observed in a wide variety of animals. We investigated this basic form of vocal control in the cotton-top tamarin (Saguinus oedipus) by measuring the amplitude of a contact call, the combination long call (CLC), while simultaneously varying the background noise level. All subjects showed a significant increase in call amplitude and syllable duration in response to an increase in background noise amplitude. Together with prior results, this study shows that tamarins have greater vocal control in the context of auditory feedback perturbation than previously suspected.

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    11/23/06 | Stereochemically general approach to adjacent bis(tetrahydrofuran) cores of annonaceous acetogenins.
    Wysocki LM, Dodge MW, Voight EA, Burke SD
    Organic Letters. 2006 Nov 23;8(24):5637-40. doi: 10.1021/ol062390l

    A series of six 2,5-disubstituted adjacent bis(tetrahydrofuran) stereoisomers with trans/erythro/cis, trans/threo/trans, or cis/threo/cis relative stereochemistry have been synthesized from known dihydroxycyclooctenes via ring opening/cross metathesis and Pd(0)-mediated asymmetric double cycloetherification. The stereochemistry of four of these isomers has been found in the biologically active annonaceous acetogenin natural products. [reaction: see text].

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    Zuker Lab
    11/16/06 | The receptors and cells for mammalian taste.
    Chandrashekar J, Hoon MA, Ryba NJ, Zuker CS
    Nature. 2006 Nov 16;444(7117):288-94. doi: 10.1038/nature05401

    The emerging picture of taste coding at the periphery is one of elegant simplicity. Contrary to what was generally believed, it is now clear that distinct cell types expressing unique receptors are tuned to detect each of the five basic tastes: sweet, sour, bitter, salty and umami. Importantly, receptor cells for each taste quality function as dedicated sensors wired to elicit stereotypic responses.

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    Murphy Lab
    11/09/06 | Network variability limits stimulus-evoked spike timing precision in retinal ganglion cells.
    Murphy GJ, Rieke F
    Neuron. 2006 Nov 9;52(3):511-24. doi: 10.1016/j.neuron.2006.09.014

    Visual, auditory, somatosensory, and olfactory stimuli generate temporally precise patterns of action potentials (spikes). It is unclear, however, how the precision of spike generation relates to the pattern and variability of synaptic input elicited by physiological stimuli. We determined how synaptic conductances evoked by light stimuli that activate the rod bipolar pathway control spike generation in three identified types of mouse retinal ganglion cells (RGCs). The relative amplitude, timing, and impact of excitatory and inhibitory input differed dramatically between On and Off RGCs. Spikes evoked by repeated somatic injection of identical light-evoked synaptic conductances were more temporally precise than those evoked by light. However, the precision of spikes evoked by conductances that varied from trial to trial was similar to that of light-evoked spikes. Thus, the rod bipolar pathway modulates different RGCs via unique combinations of synaptic input, and RGC temporal variability reflects variability in the input this circuit provides.

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    11/09/06 | Optimal information storage in noisy synapses under resource constraints.
    Varshney LR, Sjöström PJ, Chklovskii DB
    Neuron. 2006 Nov 9;52(3):409-23. doi: 10.1371/journal.pcbi.1001066

    Experimental investigations have revealed that synapses possess interesting and, in some cases, unexpected properties. We propose a theoretical framework that accounts for three of these properties: typical central synapses are noisy, the distribution of synaptic weights among central synapses is wide, and synaptic connectivity between neurons is sparse. We also comment on the possibility that synaptic weights may vary in discrete steps. Our approach is based on maximizing information storage capacity of neural tissue under resource constraints. Based on previous experimental and theoretical work, we use volume as a limited resource and utilize the empirical relationship between volume and synaptic weight. Solutions of our constrained optimization problems are not only consistent with existing experimental measurements but also make nontrivial predictions.

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    11/01/06 | Boundary enhancement and speckle reduction for ultrasound images via salient structure extraction.
    Xie J, Jiang Y, Tsui H, Heng P
    IEEE Transactions on Bio-Medical Engineering. 2006 Nov;53(11):2300-9. doi: 10.1109/TBME.2006.878088

    In this paper, we present an approach for medical ultrasound (US) image enhancement. It is based on a novel perceptual saliency measure which favors smooth, long curves with constant curvature. The perceptual salient boundaries of tissues in US images are enhanced by computing the saliency of directional vectors in the image space, via a local searching algorithm. Our measure is generally determined by curvature changes, intensity gradient and the interaction of neighboring vectors. To restrain speckle noise during the enhancement process, an adaptive speckle suspension term is also combined into the proposed saliency measure. The results obtained on both simulated images and medical US data reveal superior performance of the novel approach over a number of commonly used speckle filters. Applications of US image segmentation show that although the proposed algorithm cannot remove the speckle noise completely and may discard weak anatomical structures in some case, it still provides a considerable gain to US image processing for computer-aided diagnosis.

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    11/01/06 | Cluster analysis and robust use of full-field models for sonar beamforming
    Brian Tracey , Nigel Lee , Srinivas Turaga
    Journal of Acoustical Society of America . 11/2006;120(5): 2635–2647. doi: 10.1121/1.2346128

    Multipath propagation in shallow water can lead to mismatch losses when single-path replicas are usedfor horizontal array beamforming.Matched field processing(MFP) seeks to remedy this by using full-fieldacoustic propagationmodels to predict the multipath arrival structure. Ideally MFP can give source localization in range and depth as well as detection gains but robustly estimating range and depth is difficult in practice. The approach described here seeks to collapse full-field replica outputs to bearing which is robustly estimated while retaining any signal gains provided by the full-field model.Clusteranalysis is used to group together full-field replicas with similar responses. This yields a less redundant “sampled field” describing a set of representative multipath structures for each bearing. A detection algorithm is introduced that uses clustering to collapse beamformer outputs to bearing such that signal gains are retained while increases in the noise floor are minimized. Horizontal array data from SWELLEX-96 are used to demonstrate the detection benefits of sampled field as compared to single-pathbeamforming.

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