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PubMed2001

Two compound replication origins in Saccharomyces cerevisiae contain redundant origin recognition complex binding sites.

While many of the proteins involved in the initiation of DNA replication are conserved between yeasts and metazoans, the structure of the replication origins themselves has appeared to be different. As typified by ARS1, replication origins in Saccharomyces cerevisiae are <150 bp long and have a simple modular structure, consisting of a single binding site for the origin recognition complex, the replication initiator protein, and one or more accessory sequences. DNA replication initiates from a discrete site. While the important sequences are currently less well defined, metazoan origins appear to be different. These origins are large and appear to be composed of multiple, redundant elements, and replication initiates throughout zones as large as 55 kb. In this report, we characterize two S. cerevisiae replication origins, ARS101 and ARS310, which differ from the paradigm. These origins contain multiple, redundant binding sites for the origin recognition complex. Each binding site must be altered to abolish origin function, while the alteration of a single binding site is sufficient to inactivate ARS1. This redundant structure may be similar to that seen in metazoan origins.

Base Sequence↗
PubMed1996

Redundancy of conventional articular response variables used in juvenile chronic arthritis clinical trials.

OBJECTIVE: To estimate the degree of redundancy among articular response variables used routinely in juvenile chronic arthritis (JCA) clinical trials. METHODS: We obtained data from a large, computerised databank holding information from multiple clinical trials in children with JCA to determine Pearson correlation coefficients for changes from baseline values in articular response variables. All 508 JCA patients who entered the analysis of efficacy of the original trials were included in the present study. An r value of 0.7 or greater was considered evidence of colinearity. RESULTS: When changes in joint counts of articular manifestations were compared with changes in the respective severity scores (for example swollen joint count versus swelling severity score), the r values were always > or = 0.7. Three articular response variables related to the assessment of pain are all highly correlated with each other. The number of joints with active arthritis was correlated with the number of joints with swelling and the swelling score. Change in the overall severity score was highly correlated (r > or = 0.7) with change in nearly all articular response variables. CONCLUSIONS: Many endpoints reported in JCA trials are redundant, especially counts and scores of the same articular measure. Eliminating redundant variables would provide the same information with less complexity, and decrease the probability of statistical error and ambiguous results.

Arthritis, Juvenile↗
PubMed2003

Consensus and contention regarding redundant publications in clinical research: cross-sectional survey of editors and authors.

OBJECTIVES: To examine the perspectives of journal editors and authors on overlapping and redundant publications in clinical research. DESIGN: Pretested cross-sectional survey, containing both forced choice and open ended questions, administered by mail to the senior editors (N=99) and one randomly selected author (N=99) from all journals in the Abridged Index Medicus (1996) that published clinical research. MAIN MEASUREMENTS: The views of editors and authors about the extent of redundant publications, why they occur, how to prevent and respond to cases, and when the publication of overlapping manuscripts is justified. RESULTS: Seventy two per cent (N=71) of editors and 65% (N=64) of authors completed the survey. There was consensus between both groups that redundant publications occur because authors feel the pressure to publish and journals do not do enough to publicise, criticise, and punish cases, and that the publication of most types of overlapping articles is unacceptable. Sixty seven per cent of authors but only 31% of editors felt, however, that it was justified to publish an overlapping article in a non-peer reviewed symposium supplement, and 68% of editors but 39% of authors supported imposing restrictions on guilty authors' future submissions. In written comments, 15% to 30% of both groups emphasised that it was justified to publish overlapping articles when there were different or non-English-speaking audiences, new data, strengthened methods, or disputed findings. CONCLUSIONS: Editors, authors, and other academic leaders should together develop explicit guidelines that clarify points of contention and ambiguity regarding overlapping manuscripts.

Adult↗
PubMed1995

Does voluntary redundancy affect general practice consultation rates?

This paper presents a retrospective case control study of the General Practice consultation rates of 58 soldiers made voluntarily redundant. The redundees were compared over 140 days prior to the announcements of redundancy and 140 days after the announcements. No difference in consultation rates was found between the groups suggesting that voluntary redundancy in the Army has no effect on health and health seeking behaviour.

Adult↗
PubMed2003

Coronary blood flow regulation in exercising swine involves parallel rather than redundant vasodilator pathways.

In dogs, only combined blockade of vasodilator pathways [via adenosine receptors, nitric oxide synthase (NOS) and ATP-sensitive K+ (KATP) channels] results in impairment of metabolic vasodilation, which suggests a redundancy design of coronary flow regulation. Conversely, in swine and humans, blocking KATP channels, adenosine receptors, or NOS each impairs coronary blood flow (CBF) at rest and during exercise. Consequently, we hypothesized that these vasodilators act in parallel rather than in redundancy to regulate CBF in swine. Swine exercised on a treadmill (0-5 km/h), during control and after blockade of KATP channels (with glibenclamide), adenosine receptors [with 8-phenyltheophylline (8-PT)], and/or NOS [with Nomega-nitro-l-arginine (l-NNA)]. l-NNA, 8-PT, and glibenclamide each reduced myocardial O2 delivery and coronary venous O2 tension. These effects of l-NNA, 8-PT, and glibenclamide were not modified by simultaneous blockade of the other vasodilators. Combined blockade of KATP channels and adenosine receptors with or without NOS inhibition was associated with increased H+ production and impaired myocardial function. However, despite an increase in O2 extraction to >90% during administration of l-NNA + 8-PT + glibenclamide, vasodilator reserve could still be recruited during exercise. Thus in awake swine, loss of KATP channels, adenosine, or NO is not compensated for by increased participation of the other two vasodilator mechanisms. These findings suggest a parallel rather than a redundancy design of CBF regulation in the porcine circulation.

ATP-Binding Cassette Transporters↗
PubMed2006

Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data.

BACKGROUND: Due to the large number of genes in a typical microarray dataset, feature selection looks set to play an important role in reducing noise and computational cost in gene expression-based tissue classification while improving accuracy at the same time. Surprisingly, this does not appear to be the case for all multiclass microarray datasets. The reason is that many feature selection techniques applied on microarray datasets are either rank-based and hence do not take into account correlations between genes, or are wrapper-based, which require high computational cost, and often yield difficult-to-reproduce results. In studies where correlations between genes are considered, attempts to establish the merit of the proposed techniques are hampered by evaluation procedures which are less than meticulous, resulting in overly optimistic estimates of accuracy. RESULTS: We present two realistically evaluated correlation-based feature selection techniques which incorporate, in addition to the two existing criteria involved in forming a predictor set (relevance and redundancy), a third criterion called the degree of differential prioritization (DDP). DDP functions as a parameter to strike the balance between relevance and redundancy, providing our techniques with the novel ability to differentially prioritize the optimization of relevance against redundancy (and vice versa). This ability proves useful in producing optimal classification accuracy while using reasonably small predictor set sizes for nine well-known multiclass microarray datasets. CONCLUSION: For multiclass microarray datasets, especially the GCM and NCI60 datasets, DDP enables our filter-based techniques to produce accuracies better than those reported in previous studies which employed similarly realistic evaluation procedures.

Animals↗
PubMed2005

A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects.

BACKGROUND: As farming of Atlantic salmon is growing as an aquaculture enterprise, the need to identify the genomic mechanisms for specific traits is becoming more important in breeding and management of the animal. Traits of importance might be related to growth, disease resistance, food conversion efficiency, color or taste. To identify genomic regions responsible for specific traits, genomic large insert libraries have previously proven to be of crucial importance. These large insert libraries can be screened using gene or genetic markers in order to identify and map regions of interest. Furthermore, large-scale mapping can utilize highly redundant libraries in genome projects, and hence provide valuable data on the genome structure. RESULTS: Here we report the construction and characterization of a highly redundant bacterial artificial chromosome (BAC) library constructed from a Norwegian aquaculture strain male of Atlantic salmon (Salmo salar). The library consists of a total number of 305,557 clones, in which approximately 299,000 are recombinants. The average insert size of the library is 188 kbp, representing 18-fold genome coverage. High-density filters each consisting of 18,432 clones spotted in duplicates have been produced for hybridization screening, and are publicly available 1. To characterize the library, 15 expressed sequence tags (ESTs) derived overgos and 12 oligo sequences derived from microsatellite markers were used in hybridization screening of the complete BAC library. Secondary hybridizations with individual probes were performed for the clones detected. The BACs positive for the EST probes were fingerprinted and mapped into contigs, yielding an average of 3 contigs for each probe. Clones identified using genomic probes were PCR verified using microsatellite specific primers. CONCLUSION: Identification of genes and genomic regions of interest is greatly aided by the availability of the CHORI-214 Atlantic salmon BAC library. We have demonstrated the library's ability to identify specific genes and genetic markers using hybridization, PCR and fingerprinting experiments. In addition, multiple fingerprinting contigs indicated a pseudo-tetraploidity of the Atlantic salmon genome. The highly redundant CHORI-214 BAC library is expected to be an important resource for mapping and sequencing of the Atlantic salmon genome.

Animals↗
PubMed2001

Multiple redundant sequence elements within the fission yeast ura4 replication origin enhancer.

BACKGROUND: Some origins in eukaryotic chromosomes fire more frequently than others. In the fission yeast, Schizosaccharomyces pombe, the relative firing frequencies of the three origins clustered 4-8 kbp upstream of the ura4 gene are controlled by a replication enhancer - an element that stimulates nearby origins in a relatively position-and orientation-independent fashion. The important sequence motifs within this enhancer were not previously localized. RESULTS: Systematic deletion of consecutive segments of approximately 50, approximately 100 or approximately 150 bp within the enhancer and its adjacent core origin (ars3002) revealed that several of the approximately 50-bp stretches within the enhancer contribute to its function in partially redundant fashion. Other stretches within the enhancer are inhibitory. Some of the stretches within the enhancer proved to be redundant with sequences within core ars3002. Consequently the collection of sequences important for core origin function was found to depend on whether the core origin is assayed in the presence or absence of the enhancer. Some of the important sequences in the core origin and enhancer co-localize with short runs of adenines or thymines, which may serve as binding sites for the fission yeast Origin Recognition Complex (ORC). Others co-localize with matches to consensus sequences commonly found in fission yeast replication origins. CONCLUSIONS: The enhancer within the ura4 origin cluster in fission yeast contains multiple sequence motifs. Many of these stimulate origin function in partially redundant fashion. Some of them resemble motifs also found in core origins. The next step is to identify the proteins that bind to these stimulatory sequences.

Journal Article↗
PubMed1980

Suggested pathological basis of "redundant nerve root syndrome" of the cauda equina.

A clinical entity described as "redundant nerve root syndrome" of the cauda equina is reviewed. Eighteen reported cases with typical gross features are analyzed. Considerable speculation has existed regarding the pathogenesis of this syndrome, chiefly because the involved nerve root was not biopsied in the majority of instances. In one reported case, when the redundant root was examined histologically, a plexiform neurofibroma was found to be the cause of the thickening and redundancy of the nerve. In the case presented here, the enlarged nerve roots were part of a malignant plexiform neurofibroma with a short clinical course, and the tumor led to the death of the patient. It is suggested that biopsy of the involved nerve root is crucial in establishing the definitive diagnosis.

Adult↗
PubMed1989

Redundant nerve roots of the cauda equina: clinical aspects and consideration of pathogenesis.

In order to investigate the clinical significance of redundant nerve roots of the cauda equina (RNR) and their pathogenesis, the following studies were performed: 1) examination of 1,256 myelograms of patients with lumbar disease; 2) clinical analysis of 55 patients with RNR and 75 without RNR; 3) electrophysiological examination of 9 patients with RNR; and 4) anatomical and histopathological examination of 6 autopsy cases. RNR were found in 42% of patients with severely constricted spinal canals. In comparing patients with RNR and those without RNR, RNR were found in older patients, these patients exhibited a longer period from the onset of the symptoms to the time of myelographic manifestation, and they caused more severe signs and symptoms. The spatial distribution of redundant nerve roots and the extent of degeneration of nerve fibers in redundant nerve roots indicated the close causal relationship between RNR and constriction of the spinal canal. As the pathogenesis of RNR, the authors suggest a squeezing force from the constricted spinal canal acting on the nerve roots.

Adolescent↗
PubMed2002

Evidence for differential and redundant function of the Sox genes Dichaete and SoxN during CNS development in Drosophila.

Group B Sox-domain proteins encompass a class of conserved DNA-binding proteins expressed from the earliest stages of metazoan CNS development. In all higher organisms studied to date, related Group B Sox proteins are co-expressed in the developing CNS; in vertebrates there are three (Sox1, Sox2 and Sox3) and in Drosophila there are two (SoxNeuro and Dichaete). It has been suggested there may be a degree of functional redundancy in Sox function during CNS development. We describe the CNS phenotype of a null mutation in the Drosophila SoxNeuro gene and provide the first direct evidence for both redundant and differential Sox function during CNS development in Drosophila. In the lateral neuroectoderm, where SoxNeuro is uniquely expressed, SoxNeuro mutants show a loss or reduction of achaete expression as well as a loss of many correctly specified lateral neuroblasts. By contrast, in the medial neuroectoderm, where the expression of SoxNeuro and Dichaete overlaps, the phenotypes of both single mutants are mild. In accordance with an at least partially redundant function in that region, SoxNeuro/Dichaete double mutant embryos show a severe neural hypoplasia throughout the central nervous system, as well as a dramatic loss of achaete expressing proneural clusters and medially derived neuroblasts. However, the finding that Dichaete and SoxN exhibit opposite effects on achaete expression within the intermediate neuroectoderm demonstrates that each protein also has region-specific unique functions during early CNS development in the Drosophila embryo.

Animals↗
PubMed2003

Shared, unique and redundant functions of three members of the class I myosins (MyoA, MyoB and MyoF) in motility and chemotaxis in Dictyostelium.

Most cell types express two distinct forms of myosin I, amoeboid and short, distinguished by differences in their tail domains. Both types of myosin I have been implicated in the regulation of pseudopod formation in Dictyostelium discoideum. We examined three members of the myosin I family, one amoeboid, MyoB, and two short, MyoA and MyoB, for shared, unique and redundant functions in motility and chemotaxis. We used computer-assisted methods for reconstructing and motion analyzing cells, and experimental protocols for assessing the basic motile behavior of mutant cells in buffer and the responses of these cells to the individual spatial, temporal and concentration components of the natural wave of the chemoattractant cAMP. Analysis of both single and double mutants revealed that all three myosins play independent roles in suppressing lateral pseudopod formation in buffer and during chemotaxis. One, MyoB, also plays a unique role in priming cells to respond to the increasing temporal cAMP gradient in the front of a wave, while MyoF plays a unique role in maintaining the elongate, polarized shape of a cell in buffer, during chemotaxis in a spatial gradient of cAMP and in the front of a cAMP wave. Finally, MyoA and MyoF play redundant roles in the velocity response to the increasing temporal cAMP gradient in the front of a wave. These results, therefore, reveal an unexpected variety of shared, unique and redundant functions of the three class I myosins in motility and chemotaxis. Interestingly, the combined defects of the myosin I mutants are similar to those of a single mutant with constitutive PKA activity, suggesting that PKA plays a role in the regulation of all three class I myosins.

Animals↗
PubMed1987

Predictability and redundancy of natural images.

One aspect of human image understanding is the ability to estimate missing parts of a natural image. This ability depends on the redundancy of the representation used to describe the class of images. In 1951, Shannon [Bell. Syst. Tech. J. 30, 50 (1951)] showed how to estimate bounds on the entropy and redundancy of an information source from predictability data. The entropy, in turn, gives a measure of the limits to error-free information compaction. An experiment was devised in which human observers interactively restored missing gray levels from 128 X 128 pixel pictures with 16 gray levels. For eight images, the redundancy ranged from 46%, for a complicated picture of foliage, to 74%, for a picture of a face. For almost-complete pictures, but not for noisy pictures, this performance can be matched by a nearest-neighbor predictor.

Forecasting↗
PubMed2004

Feature selection based on mutual information and redundancy-synergy coefficient.

Mutual information is an important information measure for feature subset. In this paper, a hashing mechanism is proposed to calculate the mutual information on the feature subset. Redundancy-synergy coefficient, a novel redundancy and synergy measure of features to express the class feature, is defined by mutual information. The information maximization rule was applied to derive the heuristic feature subset selection method based on mutual information and redundancy-synergy coefficient. Our experiment results showed the good performance of the new feature selection method.

Algorithms↗
PubMed2001

Visual search for dimensionally redundant pop-out targets: evidence for parallel-coactive processing of dimensions.

In two visual search experiments, the detection of singleton feature targets redundantly defined on multiple dimensions was investigated. Targets differed from the distractors in orientation, color, or both (redundant targets). In Experiment 1, the various target types were presented either in separate blocks or in random order within blocks. Reaction times to redundant targets significantly violated the race model inequality (Miller, 1982), but only when there was constancy of the target-defining dimension(s) within trial blocks. In Experiment 2, there was dimensional variability within blocks. Consistent with Experiment 1, constancy of the target-defining dimension(s), but this time across successive trials (rather than within blocks), was critical for observing violations of the race model inequality. These results provide evidence for parallel-coactive processing of multiple dimensions, consistent with the dimension-weighting account of Müller, Heller, and Ziegler (1995).

Adolescent↗
PubMed1989

Processing redundant signals: coactivation, divided attention, or what?

The evidence for and against a redundancy gain in reaction time (RT) when the target is repeated in the visual display is reviewed. We consider the relevance of redundancy gains under these circumstances to the question of whether attention can be simultaneously directed to separate locations in the visual field. In the present experiments, two capital letters were the target stimuli in a two-alternative forced-choice RT paradigm. In addition to the usual conditions of single-target trials, trials on which the target is repeated in the display, and trials on which the target occurs with a noise letter, we introduced the innovation of a condition in which both targets occur in the display. In our two experiments, RT was fastest with single-target displays and slowest with displays containing a target and a noise letter. There was no significant difference in RT to displays in which the target was repeated and displays in which both targets were presented. Both conditions showed a redundancy gain when compared with displays containing a target and a noise letter. The lack of response competition in the both-targets condition and the overall pattern of the results were well explained by a unitary attentional focus that serially processed the letters in the display. Analyses of minima and maxima RTs were consistent with this interpretation.

Adult↗
PubMed1992

Testing models of the redundant-signals effect: a warning concerning the combination-rule regression analysis.

The redundant-signals effect is the observed RT advantage for trials presenting two or more targets, as compared with trials with only one target. Two general classes of parallel-processing model have been proposed to explain this effect: race models (e.g., Raab, 1962) and coactivation models (e.g., Miller, 1982). Various distributional analyses have been used in work aimed at discriminating between these two model classes. The present study reexamined one of these tests--the combination-rule regression analysis based on variable-criterion theory (Grice, Canham, & Boroughs, 1984)--by applying it to the data from two sets of simulated experiments. One set of simulations assumed coactivation; the other set assumed an independent race on redundant-target trials. Nearly identical combination-rule values were observed in the two sets of simulations. This finding shows that the combination rule of variable-criterion theory does not discriminate between models capable of explaining the redundant-signals effect. The implications of this finding are briefly discussed.

Attention↗
PubMed1990

Redundancy phenomena are affected by response requirements.

Results are reported for two go/no-go reaction time (RT) experiments, in which the redundant targets advantage was investigated. These experiments were replications of two earlier choice reaction time (CRT) experiments, in which letter stimuli were used. Important differences between the go/no-go RT experiments and the CRT experiments were obtained. Equal and significant redundancy advantages were obtained whether redundant targets were compared with a single target presented with a noise letter or without noise. In the CRT experiments, the advantage was not obtained in the comparison with a single target presented alone. Noise letters did not slow the RTs to single targets with which they were presented as was the case with CRT. Since the differing results of the two procedures depend on the response requirements, explanation of differing CRT data in terms of perceptual or attentional concepts is probably inappropriate. The presence and absence of response competition in the two situations may be the best interpretation. The results tend to support a conclusion of the parallel processing of two letter stimuli separated spatially by as much as 3 degrees.

Adult↗