tag:www.urmc.rochester.edu,2009-01-01:/bme/2009-11-23T09:00:24.509-05:00tag:www.urmc.rochester.edu,2009-01-01:/bme/199156912009-11-16T00:00:00Z

Computer-aided diagnosis and simultaneous visualization based on independent component analysis and clustering are integrated in an intelligent system for the evaluation of small mammographic lesions in breast MRI. These techniques are tested on biomedical time-series representing breast MRI scans and enable the extraction of spatial and temporal features of dynamic MRI data stemming from patients with confirmed lesion diagnosis. By revealing regional properties of contrast-agent uptake characterized by subtle differences of signal amplitude and dynamics, these methods provide both a set of prototypical time-series and a corresponding set of cluster assignment maps which further provide a segmentation with regard to identification and regional subclassification of pathological breast tissue lesions. Both approaches lead to an increase of the diagnostic accuracy of MRI mammography by improving the sensitivity without reduction of specificity.

A Meyer-BaeseO LangeT SchlossbauerA Wismüllertag:www.urmc.rochester.edu,2009-01-01:/bme/199103652009-11-13T00:00:00Z

WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base.

TW HarrisI AntoshechkinT BieriD BlasiarJ ChanWJ ChenN De La CruzP DavisM DuesburyR FangJ FernandesM HanR KishoreR LeeHM MüllerC NakamuraP OzerskyA PetcherskiA RangarajanA RogersG SchindelmanEM Schwarzhttp://www.urmc.rochester.edu/GEBS/faculty/Edward_Schwarz.htmMA TuliK Van AukenD WangX WangG WilliamsK YookR DurbinLD SteinJ SpiethPW Sternbergtag:www.urmc.rochester.edu,2009-01-01:/bme/198948222009-11-09T00:00:00Z

There is growing evidence that the dynamics of biological systems that appear to be exponential over short time courses are in some cases better described over the long-term by power-law dynamics. A model of rate adaptation at the synapse between inner hair cells and auditory-nerve (AN) fibers that includes both exponential and power-law dynamics is presented here. Exponentially adapting components with rapid and short-term time constants, which are mainly responsible for shaping onset responses, are followed by two parallel paths with power-law adaptation that provide slowly and rapidly adapting responses. The slowly adapting power-law component significantly improves predictions of the recovery of the AN response after stimulus offset. The faster power-law adaptation is necessary to account for the "additivity" of rate in response to stimuli with amplitude increments. The proposed model is capable of accurately predicting several sets of AN data, including amplitude-modulation transfer functions, long-term adaptation, forward masking, and adaptation to increments and decrements in the amplitude of an ongoing stimulus.

MS ZilanyIC BrucePC NelsonLH Carneyhttp://www.urmc.rochester.edu/bme/people/faculty/bio/?id=229tag:www.urmc.rochester.edu,2009-01-01:/bme/198646112009-11-05T00:00:00Z

Intracellular signals associated with or triggered by integrin ligation can control cell survival, differentiation, proliferation, and migration. Despite accumulating evidence that conformational changes regulate integrin affinity to its ligands, how integrin structure regulates signal transmission from the outside to the inside of the cell remains elusive. Using fluorescence resonance energy transfer, we addressed whether conformational changes in integrin Mac-1 are sufficient to transmit outside-in signals in human neutrophils. Mac-1 conformational activation induced by ligand occupancy or activating Ab binding, but not integrin clustering, triggered similar patterns of intracellular protein tyrosine phosphorylation, including Akt phosphorylation, and inhibited spontaneous neutrophil apoptosis, indicating that global conformational changes are critical for Mac-1-dependent outside-in signal transduction. In neutrophils and myeloid K562 cells, ligand ICAM-1 or activating Ab binding promoted switchblade-like extension of the Mac-1 extracellular domain and separation of the alpha(M) and beta(2) subunit cytoplasmic tails, two structural hallmarks of integrin activation. These data suggest the primacy of global conformational changes in the generation of Mac-1 outside-in signals.

CT LefortYM HyunJB SchultzFY LawRE Waughhttp://www.urmc.rochester.edu/bme/people/faculty/bio/?id=166PA KnaufM Kimtag:www.urmc.rochester.edu,2009-01-01:/bme/198790212009-11-02T00:00:00Z

Age-related hearing loss - presbycusis - is the most common communication problem and third most prevalent chronic medical disorder of the aged. The CBA and C57BL/6 mouse strains are useful for studying features of presbycusis. The CBA loses its hearing slowly, like most humans. Because the C57 develops a rapid, high frequency hearing loss by middle age, it has an "old" ear but a relatively young brain, a model that helps separate peripheral (cochlear) from central (brain) etiologies. This field of sensory neuroscience lacks a good mouse model for the 5-10% of aged humans with normal cochlear sensitivity, but who have trouble perceiving speech in background noise. We hypothesized that F1 (CBAxC57) hybrids would have better hearing than either parental strain. Measurements of peripheral auditory sensitivity supported this hypothesis, however, a rapid decline in the auditory efferent feedback system, did not. Therefore, F1s might be an optimal model for studying cases where the peripheral hearing is quite good in old age; thereby allowing isolation of central auditory changes due to brain neurodegeneration.

RD Frisinahttp://www.urmc.rochester.edu/gebs/faculty/robert_frisina.htmA SinghM BakS BozorgR SethX Zhutag:www.urmc.rochester.edu,2009-01-01:/bme/198466262009-10-22T00:00:00Z

Vision and audition represent the outside world in spatial synergy that is crucial for guiding natural activities. Input conveying eye-in-head position is required to maintain spatial congruence since the eyes move in the head while the ears remain head-fixed. Recently, we reported that the human perception of auditory space shifts with changes in eye position. In this study, we examined whether this phenomenon is: 1) dependent upon a visual fixation reference, 2) selective for frequency-bands (high-pass and low-pass noise) related to specific auditory spatial channels, 3) matched by a shift in the perceived straight-ahead (PSA), and 4) accompanied by a spatial shift for visual and/or bi-modal (visual and auditory) targets. Subjects were tested in a dark echo-attenuated chamber with their heads fixed facing a cylindrical screen, behind which a mobile speaker/LED presented targets across the frontal field. Subjects fixated alternating reference spots (0 degrees , +/- 20 degrees ) horizontally or vertically while either localizing targets or indicating PSA using a laser pointer. Results demonstrate that the spatial shift induced by ocular eccentricity is: 1) preserved for auditory targets without a visual fixation reference, 2) generalized for all frequency-bands, and thus all auditory spatial channels, 3) paralleled by a shift in PSA, and 4) restricted to auditory space. Findings are consistent with a set-point control strategy by which eye position governs multi-model spatial alignment. The phenomenon is robust for auditory space and egocentric perception, and highlights the importance of controlling for eye position in the examination of spatial perception and behavior.

QN CuiB RazaviWE O'NeillGD Paigehttp://www.urmc.rochester.edu/web/index.cfm?event=doctor.profile.show&person_id=1000978&display=for_researcherstag:www.urmc.rochester.edu,2009-01-01:/bme/198138042009-10-09T00:00:00Z

Several psychophysical models for masked detection were evaluated using reproducible noises. The data were hit and false-alarm rates from three psychophysical studies of detection of 500-Hz tones in reproducible noise under diotic (N0S0) and dichotic (N0Spi) conditions with four stimulus bandwidths (50, 100, 115, and 2900 Hz). Diotic data were best predicted by an energy-based multiple-detector model that linearly combined stimulus energies at the outputs of several critical-band filters. The tone-plus-noise trials in the dichotic data were best predicted by models that linearly combined either the average values or the standard deviations of interaural time and level differences; however, these models offered no predictions for noise-alone responses. The decision variables of more complicated temporal models, including the models of Dau et al. [(1996a). J. Acoust. Soc. Am. 99, 3615-3622] and Breebaart et al. [(2001a). J. Acoust. Soc. Am. 110, 1074-1088], were weakly correlated with subjects' responses. Comparisons of the dependencies of each model on envelope and fine-structure cues to those in the data suggested that dependence upon both envelope and fine structure, as well as an interaction between them, is required to predict the detection results.

SA DavidsonRH GilkeyHS ColburnLH Carneyhttp://www.urmc.rochester.edu/bme/people/faculty/bio/?id=229tag:www.urmc.rochester.edu,2009-01-01:/bme/198138032009-10-09T00:00:00Z

Subject responses were measured for individual narrow-band reproducible stimuli in a low-frequency tone-in-noise detection task. Both N0S0 and N0Spi conditions were examined. The goal of the experiment was to determine the relative importance of envelope and fine-structure cues. Therefore, chimeric stimuli were generated by recombining envelopes and fine structures from different reproducible stimuli. Detection judgments for noise-alone or tone-plus-noise stimuli that had common envelopes but different fine structures or common fine structures but different envelopes were compared. The results showed similar patterns of responses to stimuli that shared envelopes, indicating the importance of envelope cues; however, fine-structure cues were also shown to be important. The relative weight assigned to envelope and fine-structure cues varied across subjects and across interaural conditions. The results also indicated that envelope and fine-structure information are not processed independently. Implications for monaural and binaural models of masking are discussed.

SA DavidsonRH GilkeyHS ColburnLH Carneyhttp://www.urmc.rochester.edu/bme/people/faculty/bio/?id=229tag:www.urmc.rochester.edu,2009-01-01:/bme/197762882009-09-24T00:00:00Z

Recent studies have described vestibular responses in the dorsal medial superior temporal area (MSTd), a region of extrastriate visual cortex thought to be involved in self-motion perception. The pathways by which vestibular signals are conveyed to area MSTd are currently unclear, and one possibility is that vestibular signals are already present in areas that are known to provide visual inputs to MSTd. Thus, we examined whether selective vestibular responses are exhibited by single neurons in the middle temporal area (MT), a visual motion-sensitive region that projects heavily to area MSTd. We compared responses in MT and MSTd to three-dimensional rotational and translational stimuli that were either presented using a motion platform (vestibular condition) or simulated using optic flow (visual condition). When monkeys fixated a visual target generated by a projector, half of MT cells (and most MSTd neurons) showed significant tuning during the vestibular rotation condition. However, when the fixation target was generated by a laser in a dark room, most MT neurons lost their vestibular tuning whereas most MSTd neurons retained their selectivity. Similar results were obtained for free viewing in darkness. Our findings indicate that MT neurons do not show genuine vestibular responses to self-motion; rather, their tuning in the vestibular rotation condition can be explained by retinal slip due to a residual vestibulo-ocular reflex. Thus, the robust vestibular signals observed in area MSTd do not arise through inputs from area MT.

SA ChowdhuryK TakahashiGC DeAngelishttp://www.urmc.rochester.edu/gebs/faculty/greg_deangelis.htmDE Angelaki