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PubMed2005

Redundancy gain with static versus moving hands: a test of the hemispheric coactivation model.

A simple reaction time (RT) experiment was conducted to test the hypothesis that redundancy gain arises partly because of hemispheric coactivation. Stimuli were presented to the left or right of fixation, or redundantly to both, and the participants had to make keypress responses as rapidly as possible to stimulus onset. A "static" condition, in which the participants held their hands at rest, was compared with a "dynamic" condition, in which they moved their hands back and forth in an oscillating motion prior to stimulus onset. As predicted from the hypothesis of hemispheric coactivation, redundancy gain, measured as the decrease in mean RT to redundant stimuli as compared with single stimuli, was smaller in the dynamic condition than in the static one.

Adult↗

PubMed2004

Exploratory case method to determine the frequency of redundant orders within manually consolidated order lists.

A computerized provider order entry (CPOE) system can provide an efficient means of retrieving and consolidating order lists from multiple electronic clinical practice standards and protocols. However, the consolidated order list may contain exact duplicate or overlapping orders. Benner's framework for levels of nursing expertise can be used to explicate the variability of the nurse's responses to redundancies in order lists and the potential compromise to patient safety. An exploratory case method was performed to consolidate 74 orders from 11 sources. The consolidated order list contained 35% fewer orders after the redundant orders were removed. Our work has shown that many redundant orders may arise by consolidating order lists from multiple electronic standards. It is imperative that consolidated electronic order lists be manageable by the nurse according to their level of clinical and computer expertise, and that redundant orders are resolved before being displayed to the nurse.

Humans↗

PubMed2006

Reduction of information redundancy in the ascending auditory pathway.

Information processing by a sensory system is reflected in the changes in stimulus representation along its successive processing stages. We measured information content and stimulus-induced redundancy in the neural responses to a set of natural sounds in three successive stations of the auditory pathway-inferior colliculus (IC), auditory thalamus (MGB), and primary auditory cortex (A1). Information about stimulus identity was somewhat reduced in single A1 and MGB neurons relative to single IC neurons, when information is measured using spike counts, latency, or temporal spiking patterns. However, most of this difference was due to differences in firing rates. On the other hand, IC neurons were substantially more redundant than A1 and MGB neurons. IC redundancy was largely related to frequency selectivity. Redundancy reduction may be a generic organization principle of neural systems, allowing for easier readout of the identity of complex stimuli in A1 relative to IC.

Acoustic Stimulation↗

PubMed2006

Unequal genetic redundancies in Arabidopsis--a neglected phenomenon?

Genetic redundancy is a common phenomenon in Arabidopsis and is thought to be responsible for the absence of phenotypes in the majority of single loss-of-function mutants. In this review, we highlight an increasing number of examples in which redundancy between homologous genes is limited or absent despite functional equivalence of the respective proteins. In particular, we focus on cases of unequal redundancy, where the absence of a mutant phenotype in loss-of-function mutants of one gene contrasts with a strong phenotype in mutants of its homolog. In the double mutants, this phenotype is strongly enhanced. Possible explanations for such scenarios are discussed. We propose that the study of unequally redundant gene pairs offers a unique opportunity to understand global patterns of functional genome evolution.

Arabidopsis↗

PubMed2006

Multiple redundant Wnt signaling components function in two processes during C. elegans vulval development.

In Caenorhabditis elegans, vulval precursor cell (VPC) fate is specified by the action of RTK/Ras, Notch and Wnt signaling pathways. While the identity of signals for the Ras and Notch pathways is known, the source and identity of the Wnt ligand acting on the VPCs are unknown. Single mutations in any of the five Wnt genes (lin-44, cwn-1, cwn-2, egl-20 and mom-2) do not cause strong defects in VPC fate specification, suggesting that functionally redundant Wnts are required. Surprisingly, we found that all five Wnts influence VPC fate. The strongest defects we observed were in the lin-44; cwn-1; egl-20 triple mutant. Anterior VPCs were more strongly affected by loss of Wnt function than posterior VPCs, and expression from WntColon, two colonsGFP transcriptional reporters showed that the Wnts most strongly affecting VPC fate were expressed predominantly in the posterior, suggesting that some of the redundant Wnt ligands act over a distance to affect the VPCs. In addition to ligand redundancy, we found that at least three Wnt receptors, lin-17, mom-5 and mig-1, function in the VPCs. We also examined ligand and receptor function in another Wnt-mediated vulval process, the orientation of the P7.p lineage. Here, too, we found that four of five Wnt receptors can influence P7.p orientation, suggesting that a surprising amount of functional redundancy exists in Wnt signaling during C. elegans vulval induction.

Animals↗

PubMed2000

Intersensory redundancy guides attentional selectivity and perceptual learning in infancy.

This study assessed an intersensory redundancy hypothesis, which holds that in early infancy information presented redundantly and in temporal synchrony across two sense modalities selectively recruits attention and facilitates perceptual differentiation more effectively than does the same information presented unimodally. Five-month-old infants' sensitivity to the amodal property of rhythm was examined in 3 experiments. Results revealed that habituation to a bimodal (auditory and visual) rhythm resulted in discrimination of a novel rhythm, whereas habituation to the same rhythm presented unimodally (auditory or visual) resulted in no evidence of discrimination. Also, temporal synchrony between the bimodal auditory and visual information was necessary for rhythm discrimination. These findings support an intersensory redundancy hypothesis and provide further evidence for the importance of redundancy for guiding and constraining early perceptual learning.

Attention↗

PubMed2005

Age-related differences in the processing of redundant visual dimensions.

Age differences in the redundant-signals effect and coactivation of visual dimensions were investigated in 2 experiments. In Experiment 1 the task required the conjoining of dimensions, whereas in Experiment 2 the spatial separation of dimensions was manipulated. Although coactivation was evident for both age groups when the redundant dimensions occurred at the same location, older adults showed more evidence for coactivation, perhaps because of compensation for declines in perceptual processing. When the redundant dimensions were separated, neither age group showed evidence for coactivation. These findings indicate that the coactive processing of redundant visual dimensions is spared in healthy older adults and that for both groups, attention must be focused on both dimensions for coactivation to occur.

Aged↗

PubMed2004

Towards full employment: using RNAi to find roles for the redundant.

Cancer is a genetic disease that ultimately results from the failure of cells to respond correctly to diverse signals. Signal transduction and signal integration are highly complex, requiring the combinatorial interaction of multiple genes. Classical genetics in model organisms including Caenorhabditis elegans has been of immense use in identifying nonredundant components of conserved signalling pathways. However, it is likely that there is much functional redundancy in the informational processing machinery of metazoan cells; we therefore need to develop methods for uncovering such redundant functions in model organisms if we are to use them to understand complex gene interactions and oncogene cooperation. RNAi may provide a powerful tool to probe redundancy in informational networks. In this review, I set out some of the progress made so far by classical genetics in understanding redundancy in gene networks, and outline how RNAi may allow us to approach this problem more systematically in C. elegans. In particular, I discuss the use of genome-wide RNAi screens in C. elegans to identify synthetic lethal interactions and compare this with synthetic lethal interaction analysis in Saccharomyces cerevisiae.

Animals↗

PubMed2006

Controlling chaotic robots with kinematical redundancy.

Robots with kinematical redundancy under the pseudoinverse control exhibit undesirable chaotic joint motion, which leads to erratic behaviors. In this study, we used the delayed feedback method to control chaotic motions of a planar 3R rigid and a planar 3R flexible redundant robot under the pseudoinverse control when the end-effector traces a closed-path repeatedly in the work space. It was demonstrated that chaotic motions of robots with kinematical redundancy can be turned into regular motion when the delayed feedback method was applied with some appropriate parameters. This study provides a new insight helpful to solve the repeatability problem of redundant manipulators.

Biomechanical Phenomena↗

PubMed1999

Measures of degeneracy and redundancy in biological networks.

Degeneracy, the ability of elements that are structurally different to perform the same function, is a prominent property of many biological systems ranging from genes to neural networks to evolution itself. Because structurally different elements may produce different outputs in different contexts, degeneracy should be distinguished from redundancy, which occurs when the same function is performed by identical elements. However, because of ambiguities in the distinction between structure and function and because of the lack of a theoretical treatment, these two notions often are conflated. By using information theoretical concepts, we develop here functional measures of the degeneracy and redundancy of a system with respect to a set of outputs. These measures help to distinguish the concept of degeneracy from that of redundancy and make it operationally useful. Through computer simulations of neural systems differing in connectivity, we show that degeneracy is low both for systems in which each element affects the output independently and for redundant systems in which many elements can affect the output in a similar way but do not have independent effects. By contrast, degeneracy is high for systems in which many different elements can affect the output in a similar way and at the same time can have independent effects. We demonstrate that networks that have been selected for degeneracy have high values of complexity, a measure of the average mutual information between the subsets of a system. These measures promise to be useful in characterizing and understanding the functional robustness and adaptability of biological networks.

Animals↗

PubMed1984

Visual-motor processing: relationships among age, dimensional variation, and the use of information redundancy.

This study examined the hypothesis that age-related superiority in the ability to process complex stimuli was linked with age differences in the use of information redundancy. Seventy-two children (6-9 years of age) solved a series of puzzles that varied in complexity and redundancy. Significant correlations between age and completion times were found only for those puzzles that included some degree of information redundancy. Completion times on multidimensional puzzles that lacked redundancy were not significantly age related.

Age Factors↗

PubMed1998

Increment of efficiency in the identification of noble genes by colony hybridization assay. (Screening of low redundant clones from human fetal cDNA library).

For the rapid identification of noble genes in a specific tissue by computer analysis from the cDNA sequences determined by single-pass cDNA sequencing, clone redundancy was one of the major obstacles. To facilitate the efficiency in identification of noble genes, it was necessary to reduce the number of clones to be sequenced by eliminating the redundant clones for a rapid analysis. In order to increase the probability of isolating noble sequences from the cDNA clones of human fetal liver tissue origin, colony hybridization assay was adopted and redundant clones were efficiently removed. Four cDNA clones highly redundant in the human fetal liver cDNA libraries including alpha-globin, gamma-globin, serum albumin and H19 RNA sequences were selected as the probes. Two hundreds and sixty two cDNA clones were randomly selected and tested with the probes for hybridization properties. The identity of each cDNA clone giving positive or negative signals in the hybridization assay was determined by DNA homology search with the nucleic acid databases. Among the 76 clones giving positive signals, 57 clones (75%) were found to be identical to the probe sequences and could be eliminated by colony hybridization assay before neucleotide sequencing.

Cloning, Molecular↗

PubMed2000

A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries.

For comprehensive analysis of genes expressed in the model dicotyledonous plant, Arabidopsis thaliana, expressed sequence tags (ESTs) were accumulated. Normalized and size-selected cDNA libraries were constructed from aboveground organs, flower buds, roots, green siliques and liquid-cultured seedlings, respectively, and a total of 14,026 5'-end ESTs and 39,207 3'-end ESTs were obtained. The 3'-end ESTs could be clustered into 12,028 non-redundant groups. Similarity search of the non-redundant ESTs against the public non-redundant protein database indicated that 4816 groups show similarity to genes of known function, 1864 to hypothetical genes, and the remaining 5348 are novel sequences. Gene coverage by the non-redundant ESTs was analyzed using the annotated genomic sequences of approximately 10 Mb on chromosomes 3 and 5. A total of 923 regions were hit by at least one EST, among which only 499 regions were hit by the ESTs deposited in the public database. The result indicates that the EST source generated in this project complements the EST data in the public database and facilitates new gene discovery.

Arabidopsis↗

PubMed2005

Redundancy gain and coactivation in bimodal detection: evidence for the preservation of coactive processing in older adults.

Previous investigations of adult age differences in the redundant signals effect suggest that both older and younger adults benefit from the presentation of redundant information. However, age deficits in divided attention may cause older adults to process redundant information in a different manner. In the present experiment, we tested between two competing explanations for the redundant signals effect: separate activation and coactivation. To investigate this issue, we used a bimodal detection task in which the auditory signal was a 1000-Hz tone and the visual signal was an asterisk. Both age groups showed significant violations of Miller's race model inequality, providing evidence for coactivation. These results suggest that, despite age-related deficits in divided attention, the ability to coactivate information from bimodal signals is spared with increased age.

Adolescent↗

PubMed2004

Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana.

Functional redundancy between duplicated genes is predicted to be transitory, as one gene either loses its function or gains a new function, or both genes accrue degenerative, yet complimentary mutations. Yet there are many examples where functional redundancy has been maintained between gene duplicates. To determine whether selection is acting on functionally redundant gene duplicates, we performed molecular evolution and population genetic analyses between two pairs of functionally redundant MADS-box genes from the model plant Arabidopsis thaliana: SEPALLATA1 (SEP1) and SEPALLATA2 (SEP2), involved in floral organ identity, and SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2), involved in seed shattering. We found evidence for purifying selection acting to constrain functional divergence between paralogous genes. The protein evolution of both pairs of duplicate genes is functionally constrained, as evidenced by Ka/Ks ratios of 0.16 between paralogs. This functional constraint is stronger in the highly conserved DNA-binding and protein-binding MIK region than in the C-terminal region. We also assayed the evolutionary forces acting between orthologs of the SEP and SHP genes in A. thaliana and the closely related species, Arabidopsis lyrata. Heterogeneity analyses of the polymorphism-to-divergence ratio indicate selective sweeps have occurred within the transcriptional unit of SHP1 and the promoter of SHP2 in the A. thaliana lineage. Similar analyses identified a significant reduction in polymorphism within the SEP1 locus, spanning the 3' region of intron 1 to exon 3, that may represent an intragenic sweep within the SEP1 locus. We discuss whether the evolutionary forces acting on SEP1 and SEP2 versus SHP1 and SHP2 vary according to their position in the floral developmental pathway, as found with other floral-regulatory genes.

Arabidopsis↗

PubMed1997

Creation and characterization of a new, non-redundant fragment data bank.

The success achieved for protein structure prediction of loop regions with insertions and deletions by knowledge-based methods depends on the quality of the underlying information, i.e. a fragment data bank as complete as possible is needed. However, the greater the number of proteins contributing to the data base the more redundant information is included, which leads to structurally similar proposals in loop predictions and to longer times for extracting fragments. So it is not only necessary to increase the number of proteins for building the loop data base but also to cluster the resulting fragments according to their structural similarities in order to remove redundancy. Here, a new, non-redundant fragment data bank is described, which is based on all proteins in the Brookhaven Protein Data Bank (release 7/95) with a resolution > or = 2.0 A and which can be updated easily by including new information from structures to be solved in the future. In the clustering process presented, the resulting clusters are optimized in several cycles until self-consistency. In this way all redundant information is removed without loosing any significantly different fragments. Finally the resulting fragment data bank is analysed with respect to its completeness.

Algorithms↗

PubMed2006

Intraguild predation reduces redundancy of predator species in multiple predator assemblage.

1. Interference between predator species frequently decreases predation rates, lowering the risk of predation for shared prey. However, such interference can also occur between conspecific predators. 2. Therefore, to understand the importance of predator biodiversity and the degree that predator species can be considered functionally interchangeable, we determined the degree of additivity and redundancy of predators in multiple- and single-species combinations. 3. We show that interference between two invasive species of predatory crabs, Carcinus maenas and Hemigrapsus sanguineus, reduced the risk of predation for shared amphipod prey, and had redundant per capita effects in most multiple- and single-species predator combinations. 4. However, when predator combinations with the potential for intraguild predation were examined, predator interference increased and predator redundancy decreased. 5. Our study indicates that trophic structure is important in determining how the effects of predator species combine and demonstrates the utility of determining the redundancy, as well as the additivity, of multiple predator species.

Amphipoda↗

PubMed2005

BAS1 and SOB7 act redundantly to modulate Arabidopsis photomorphogenesis via unique brassinosteroid inactivation mechanisms.

Active brassinosteroids (BRs), such as brassinolide (BL) and castasterone (CS), are growth-promoting plant hormones. An Arabidopsis cytochrome P450 monooxygenase (CYP734A1, formerly CYP72B1), encoded by the BAS1 gene, inactivates BRs and modulates photomorphogenesis. BAS1 was identified as the overexpressed gene responsible for a dominant, BR-deficient mutant, bas1-D. This mutant was isolated in an activation-tagged screen designed to identify redundant genes that might not be identified in classic loss-of-function screens. Here we report the isolation of a second activation-tagged mutant with a BR-deficient phenotype. The mutant phenotype is caused by the overexpression of SOB7 (CYP72C1), a homolog of BAS1. We generated single and double null-mutants of BAS1 and SOB7 to test the hypothesis that these two genes act redundantly to modulate photomorphogenesis. BAS1 and SOB7 act redundantly with respect to light promotion of cotyledon expansion, repression of hypocotyl elongation and flowering time in addition to other phenotypes not regulated by light. We also provide biochemical evidence to suggest that BAS1 and SOB7 act redundantly to reduce the level of active BRs, but have unique mechanisms. Overexpression of SOB7 results in a dramatic reduction in endogenous CS levels, and although single null-mutants of BAS1 and SOB7 have the same level of CS as the wild type, the double null-mutant has twice the amount. Application of BL to overexpression lines of BAS1 or SOB7 results in enhanced metabolism of BL, though only BAS1 overexpression lines confer enhanced conversion to 26-OHBL, suggesting that SOB7 and BAS1 convert BL and CS into unique products.

Amino Acid Sequence↗