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At least 19 recordsLinked to original sources

PubMed1976

Visual processing of nonlinguistic strings: redundancy effects and reading ability.

Visual redundancy effects were investigated in two experiments using nonalphabetic material. Experiment 1 had adult subjects search for the presence or absence of a predetermined target symbol through single six-symbol linear arrays. Reaction times were significantly faster in both a distributional redundancy and a spatial redundancy condition than in a no-redundancy condition. Experiment 2 had good and poor sixth-grade readers serve in the no-redundancy and spatial redundancy conditions of Experment 1. Poor readers were equivalent to good readers in the no-redundancy condition but were significantly slower in the spatial redundancy condition. Thus, spatial redundancy was shown to be operative in single symbol search time in a paradigm that avoided confounding by higher order linguistic variables. The present experiments, in conjunction with prior findings that good and poor readers differ in letter search time by their ability to use spatial redundancy, suggest that processes involved in the component skill of letter identification cannot be considered trivial to the reading process.

Adult↗

PubMed2025

Redundant and Singular Regulatory Elements Underlie the Rapidly Evolving Pigmentation of Drosophila.

A major hurdle in understanding the molecular changes responsible for metazoan diversity is the characterization of cis-regulatory elements (CREs) for gene regulatory networks (GRNs). CRE changes are suspected to be commonplace in trait evolution, since such changes circumvent the deleterious effects of pleiotropy. A growing list of genes, though, is known to be regulated by redundant CREs. Such redundant CRE architectures complicate the characterization of GRN evolution, as they compound the effort to characterize each locus, and raise the questions of how and whether genes with redundant architectures evolve expression. Here, we used the evolution of sexually dimorphic abdomen pigmentation of Drosophila (D.) melanogaster as a model to study the function and evolution of CREs. Numerous sequences were evaluated that were previously predicted as potential abdomen CREs. Most of these predictions were validated, including two, four, and ten that, respectively, reside in the homothorax, grainy head, and Eip74EF transcription factor loci. The homothorax CREs were found to be partially redundant for this gene's pigmentation function, and pupal-stage Homothorax expression and the CRE activities were conserved among Drosophila species with the derived dimorphic and ancestral monomorphic phenotypes. Similarly, the Eip74EF CREs were conserved in the monomorphic D. willistoni. Thus, this gene's extensive CRE spatiotemporal redundancy has been conserved for over 30 million years, predating the dimorphic trait. Pigmentation evolution has been connected elsewhere to changes in nonredundant CREs. When these traits evolve, GRN changes may be biased towards the genes with singular nonredundant CREs, while the expression of redundantly regulated genes remains conserved.

Animals↗

PubMed2026

Brief Review: Rethinking Colonic Redundancy in Gastroenterology.

BACKGROUND: Dolichocolon (DC), or colonic redundancy, is an elongated and tortuous colon described as early as 1820, yet it remains underrecognized in clinical gastroenterology. Advances in imaging and motility assessment offer new insights into its prevalence, mechanisms, and clinical implications. AIMS: To summarize current evidence on the anatomy, epidemiology, and potential clinical significance of DC and to explore possible pathophysiological mechanisms linking this variant to gastrointestinal disorders. METHODS: A targeted literature review of studies published between 1900 and 2024 was conducted using PubMed and Scopus with search terms including dolichocolon, colonic redundancy, and redundant colon. Publications addressing anatomy, motility, symptom associations, and disease relevance were included. RESULTS: Though epidemiological data are limited, it has been estimated that DC affects 10-20% of the population and is associated with constipation, volvulus, and, possibly, inflammatory bowel disease. Proposed mechanisms include segmental stasis and ischemia in redundant loops, altered neuromuscular signaling, and increased mucosal surface area promoting immune-microbiota interactions. Despite its potential importance, DC is rarely noted in modern radiology reports, contributing to under-recognition in clinical practice. CONCLUSIONS: Colonic redundancy represents a common anatomic variant with potentially overlooked clinical implications. Standardized radiologic characterization and prospective studies are needed to clarify its role in gastrointestinal disorders and to guide future diagnostic and therapeutic approaches.

Humans↗

PubMed1978

Redundant nerve roots of the cauda equina. A report of five cases.

Five personally examined cases of redundant nerve roots of the cauda equina are added to the 13 hitherto on record. Except for segmental neurological deficits, intermittent claudication-like symptoms of the cauda equina dominated the histories of four of our five cases. The diagnosis was confirmed at surgical exploration, which included laminal and dural decompression. At follow-up (two months--three years) the neurological deficit, or the intermittent claudication, or both, had improved in all our patients. The pathogenesis of root redundancy is obscure. It seems that the symptoms arise through the action of at least two factors viz compression of the spinal content and the existence of one or more redundant roots. Wider use of diagnostic aids and surgical exploration would probably show that redundant roots are more common than hitherto supposed.

Aged↗

PubMed1977

Avian myeloblastosis virus RNA is terminally redundant: implications for the mechanism of retrovirus replication.

We have determined the terminal heteropolymeric sequences of AMV RNA by the following procedures: first, RNA sequence determination on the 5' terminal and the poly(A)-linked 3' terminal T1 oligonucleotides, and second, analysis by the Maxam and Gilbert (1977) method of AMV strong stop DNA and of DNA complementary to the poly(A)-linked T1 oligonucleotide, synthesized with reverse transcriptase and (pdT)13 as primer. The structure deduced for the 5' terminal region is (5')7mGpppGmCCAUUCUACCUCUCACCACAUUGGUGUGCACCUGGGUUGAUGGCCGGACCGUCGAUUCCCUGACGACUACGAGCACCUGCAUGAAGCAGAAGGCUUCAU... Two distinct 3' terminal sequences were deduced: GCCAUUCUACCUCUCAAA...AOH and GCCAUUCUACCUCUCACCAAA...AOH. The two termini, differing by a C-C-A sequence, may reflect genetic heterogeneity of the AMV stock or, more probably, may be generated at or after RNA transcription. These results demonstrate a terminal redundancy of the hetero polymeric sequence of 16 and 19 nucleotides, respectively. The terminal redundancy allows for mechanisms which involve transfer of the DNA segment synthesized on the 5' terminal redundant sequence to the 3' terminal redundant sequence.

Alpharetrovirus↗

PubMed1976

Sequence arrangement in herpes simplex virus type 1 DNA: identification of terminal fragments in restriction endonuclease digests and evidence for inversions in redundant and unique sequences.

It has been proposed by Sheldrick and Berthelot (1974) that the terminal sequences of herpes simplex virus type 1 (HSV-1) DNA are repeated in an internal inverted form and that the inverted redundant sequences delimit and separate two unique sequences, S and L. In this study the sequence arrangement in HSV-1 DNA has been investigated with restriction endonuclease cleavage, end-labeling studies, and molecular hybridization experiments. The terminal fragments in digests with restriction endonucleases Hind III, Hpa-1, EcoRI and Bum were identified and shown to be consistent with the Sheldrick and Berthelot model. Inverted fragments which contain unique sequences as well as redundant sequences, and which the model predicts, were identified by DNA-DNA hybridization studies. Further cleavage of Bum fragments with Hpa-1 also revealed inversions of the terminal sequences that contained unique sequences. The results obtained showed that the unique sequences S and L are relatively inverted in different DNA molecules in the population, resulting in the presence of four related genomes with rearranged sequences in apparently equal amounts. The redundant sequences bounding S do not share complete sequence homology with those bounding L, but hybridization studies are presented which show that the terminal 0.3% of the genome is repeated in every redundant sequence.

Base Sequence↗

PubMed1977

Temporal patterns, their distribution and redundancy in trains of spontaneous neuronal spike intervals of the feline hippocampus studied with a non-parametric technique.

A modification of the non-parametric technique for the analysis of temporal patterns in long trains of single neuronal spike intervals has been described and tested empiracally. The technique is based on inequality testing of sequential pairs of intervals. If the second interval in a pair is longer or shorter than or equal to the first interval, a(+), a(-), and a (0) is recorded respectively in sequential bins of the computer memory. Subsequently, the long sequences of signs are arranged into transition frequency matrices which are then converted into transition probability matrices of various complexity. In this manner, the sign permutations composed of 4, 5, 6, etc. signs were studied. First of all, the theoretical distribution of various sign permutations was derived, assuming that the arrangement of intervals that generate the signs is totally independent. The theoretical distribution of signs permutations in tetragrams, pentagrams and hexagrams constitute the 'controls' with which the empirical data can be compared. In this manner, using the chi-square test, the total deviation of a studied neuronal output from an independent state can be quantified. The empirical data showed a consistent deviation from the theoretical distribution of sign permutations during REM sleep, as compared to slow wave sleep which was characterized by an almost perfect theoretical distribution of sign permutations. This indicates that slow wave sleep is associated with relaxation of constraints that are responsible for the emergence of specific patterns. In addition, redundancies in the occurrence of sign permutations, and the linear relationships between them, have been defined and tested empirically. The apparent discrepancies between the redundancies, based on theoretical symmetry in sign distribution and the linear redundancy that fits the empirical data, have been defined and discussed.

Action Potentials↗

PubMed1975

Comprehending a word: the influence of speed and redundancy on auditory comprehension in aphasia.

To assess the contribution of various factors to comprehension of a target word, an auditory comprehension test was devised and administered to a series of aphasic patients. Patients were required to select from an array that picture which corresponded to a spoken target word. Each patient heard the target word under five conditions: (1) target spoken alone; (2) target embedded in a neutral (low redundancy) sentence enunciated at a normal rate of speaking; (3) target in a neutral sentence enunciated at a slow rate of speaking; (4) target embedded in a sentence containing semantic support (high redundancy); (5) target embedded in a sentence containing a semantically-deceptive element. Semantic redundancy and rate of presentation made contributions to comprehensibility. Semantic confusions were prevalent among all aphasics but, contrary to earlier reports, posterior patients were especially prone to acoustic confusions. Except for conduction aphasics, patients were more likely to confuse words which began with the same sounds than words which ended with the same sounds. Patients with adequate comprehension at the start of the testing displayed a uniform tendency to improve on the conditions administered later, while those with impaired comprehension at the start usually did not.

Aphasia↗

PubMed1978

The role of spatial redundancy in grapheme recognition: perception or inference?

The question under investigation is whether spatial redundancy operates by restricting the number of valid alternatives at each serial position or whether it serves a perceptual function by keeping visually confusable graphemes from appearing in the same array and/or maximizing the distance between such graphemes when they do occur in the same array. The first experiment used the same-different task to establish a confusion matrix for 12 non-linguistic symbols. The spatial relation between the members of two pairs of confusable symbols was manipulated in a second experiment, which had subjects look for the presence or absence of a predetermined target symbol in single six-symbol linear arrays. Facilitation was found to be dependent upon the perceptual consequences of serial position constraint rather than upon the constraint per se. The constraint was most effective when it served to prevent members of visually confusable pairs from occurring in the same array. Since spatial redundancy may operate at the feature extraction stage by minimizing competition for the same sets of feature detectors and since words are likely to be high in spatial redundancy, the possibility is raised that part of the word superiority effect may be due to visual factors rather than to linguistic context.

Form Perception↗

PubMed1977

Permissible syndromes. The influence of redundancy on patterns of information.

A model of clinical decision according to Bayes's formula is described and the problem of redundant informations is evaluated. It is postulated that a definitory and a syndromatic redundancy are unavoidable, which is why it is necessary to develop a correction factor. A series of indicants is investigated in two populations, and it is shown that correction for redundancy results in far-reaching changes in the patterns of information. The permissible syndrome is defined: a subset of informations containing the necessary and sufficient predictive capacity. The methods described may be used for an evaluation of common syndromes and may enable comparisons of information patterns, related to identical or different criteria.

Anxiety↗

PubMed2026

A spatiotemporal resolution to genetic redundancy: MIR164 diversification coordinates development and metabolism in Brassica.

Whole-genome duplication (WGD) events create genetic redundancy, posing the evolutionary challenge of how paralogs escape functional overlap to drive innovation. Here, we demonstrate that the MIR164 family in Brassica oleracea resolves this redundancy through spatiotemporal niche partitioning. Following WGD, the family expanded to eight members, which subsequently underwent divergent selection-some preserved under purifying selection, while others showed signals of positive selection. This led to expression divergence, with Bol-MIR164a1 emerging as a key universally expressed paralog. CRISPR-Cas9 mutagenesis of Bol-MIR164a1 revealed its essential role in coordinating two pivotal traits: leaf serration and leaf coloration. Mutants exhibited enhanced leaf serration due to spatial deregulation of CUC2 at organ boundaries, concurrently with yellow-green leaves and elevated flavonoid accumulation. We mechanistically linked the metabolic phenotype to direct transactivation of the anthocyanidin reductase (ANR) promoter by NAC100, alongside its upregulation of chlorophyll catabolism genes. Our findings establish a paradigm in which spatial segregation of target gene expression domains enables a single, widely expressed miRNA paralog to resolve genetic redundancy by independently orchestrating distinct regulatory programs. This provides a fundamental framework for understanding complex trait evolution in polyploids. This allows a single miRNA locus to independently orchestrate both morphological patterning and metabolic programming, providing a fundamental framework for understanding complex trait evolution in polyploid crops.

MicroRNAs↗

PubMed1978

Redundant nerve roots of the cauda equina.

Two cases of redundant nerve roots syndrome are presented. Both cases displayed coiled and elongated nerve roots of cauda equina, associated with proliferated fibrous tissue on the ligamentum flavum or with spondylosis and disc protrusion compressing the caudal dural sac. The pathogenesis of the syndrome of redundant nerve roots is briefly discussed.

Adult↗

PubMed2025

CAGEcleaner: reducing genomic redundancy in gene cluster mining.

SUMMARY: Mining homologous biosynthetic gene clusters (BGCs) typically involves searching colocalised genes against large genomic databases. However, the high degree of genomic redundancy in these databases often propagates into the resulting hit sets, complicating downstream analyses and visualization. To address this challenge, we present CAGEcleaner, a Python-based pipeline with auxiliary bash scripts designed to reduce redundancy in gene cluster hit sets by dereplicating the genomes that host these hits. CAGEcleaner integrates seamlessly with widely used gene cluster mining tools, such as cblaster and CAGECAT, enabling efficient filtering and streamlining BGC discovery workflows. AVAILABILITY AND IMPLEMENTATION: Source code and documentation is hosted at GitHub (https://github.com/LucoDevro/CAGEcleaner) and Zenodo (https://doi.org/10.5281/zenodo.14726119) under an MIT license. For accessibility, CAGEcleaner is installable from Bioconda (https://anaconda.org/bioconda/cagecleaner) and PyPi (https://pypi.org/project/cagecleaner/), and is also available as a Docker image from DockerHub (https://hub.docker.com/r/lucodevro/cagecleaner).

Software↗

PubMed2026

MCM10 and RECQL4 have cooperative and redundant roles in activating the CMG helicase during the replication initiation.

DNA replication initiation requires activation of the CMG helicase to establish the replisome. This process involves the extrusion of single-stranded DNA (ssDNA) from the central channel of MCM double hexamers, allowing the two CMG helicases to pass each other; however, the factors that mediate this process in human cells remain unclear. We show that degron-mediated depletion of either MCM10 or RECQL4 alone causes mild replication defects, whereas simultaneous depletion of both proteins severely impairs CMG activation. ChIP-seq analyses demonstrate that RECQL4 localizes to replication initiation zones (IZs) independently of MCM10, whereas MCM10 recruitment to IZs is enhanced upon RECQL4 depletion, consistent with partially redundant roles during CMG activation. Rescue experiments further indicate that RECQL4 cooperates with MCM10 through direct interaction, and that their ssDNA-binding activity underlies their functional overlap. We propose that MCM10 and RECQL4 act cooperatively and redundantly to promote CMG activation.

CMG activation↗

PubMed1978

Absence of circularly permuted and largely redundant sequences in the genome of visna virus.

A previous study of the infectivity of visna virus proviral DNA suggested that the genetic information of the virus is distributed over at least two of the RNA subunits. Because the genetic complexity of visna virus corresponds to the size of one subunit, this result may imply that sequence redundancies exist within each subunit. In the present article we have examined this question by constructing a map of the large RNase T1-resistant oligonucleotides of the viral genome. Our principal results are as follows: (i) all 36S RNA subunits have the same genetic content regardless of their polyadenylic acid [poly(A)] content; (ii) the poly(A) tract is present at the 3' end of the molecule; and (iii) the recoveries of 19 large RNase T1-resistant oligonucleotides from poly(A)-tagged RNA fragments of various sizes demonstrate that the oligonucleotides are organized in the same linear order within all subunits. Our results, therefore, exclude the existence of large sequence redundancies in the genome of visna virus.

Base Sequence↗

PubMed2021

The Murine MHC Class II Super Enhancer IA/IE-SE Contains a Functionally Redundant CTCF-Binding Component and a Novel Element Critical for Maximal Expression.

In both humans and mice, CTCF-binding elements form a series of interacting loops across the MHC class II (MHC-II) locus, and CTCF is required for maximal MHC-II gene expression. In humans, a CTCF-bound chromatin insulator termed XL9 and a super enhancer (SE) DR/DQ-SE situated in the intergenic region between HLA-DRB1 and HLA-DQA1 play critical roles in regulating MHC-II expression. In this study, we identify a similar SE, termed IA/IE-SE, located between H2-Eb1 and H2-Aa of the mouse that contains a CTCF site (C15) and a novel region of high histone H3K27 acetylation. A genetic knockout of C15 was created and its role on MHC-II expression tested on immune cells. We found that C15 deletion did not alter MHC-II expression in B cells, macrophages, and macrophages treated with IFN-γ because of functional redundancy of the remaining MHC-II CTCF sites. Surprisingly, embryonic fibroblasts derived from C15-deleted mice failed to induce MHC-II gene expression in response to IFN-γ, suggesting that at least in this developmental lineage, C15 was required. Examination of the three-dimensional interactions with C15 and the H2-Eb1 and H2-Aa promoters identified interactions within the novel region of high histone acetylation within the IA/IE-SE (termed N1) that contains a PU.1 binding site. CRISPR/Cas9 deletion of N1 altered chromatin interactions across the locus and resulted in reduced MHC-II expression. Together, these data demonstrate the functional redundancy of the MHC-II CTCF elements and identify a functionally conserved SE that is critical for maximal expression of MHC-II genes.

Animals↗

PubMed1975

Effects of temporal grouping and redundancy level on the paired-associate learning of retarded adolescents and nonretarded children.

Institutionalized adolescents and nonretarded third-grade children were presented with sets of paired associates which differed in redundancy level and temporal grouping. Redundancy level (33 and 50 percent) was embedded in a list of paired associates by varying the number of repetitions in the response terms. The paired associates were presented temporally in blocks of twos (33 percent) or threes (50 percent). One-half of the subjects received the paired associates highly organized; i.e., all response terms of a temporal block were the same. During testing, all stimulus terms were presented simultaneously for the free-ordered recall of the response terms. For both groups, performance was superior following the more highly organized (congruent) presentation, with the performance of the nonretarded subjects exceeding that of the retarded adolescents. Comparisons were made with previous studies in this series.

Adolescent↗

PubMed1979

Features versus redundancy: comments on Massaro, Venezky, and Taylor's "Orthographic regularity, positional frequency, and visual processing of letter strings".

Massaro, Venezky, and Taylor (1979) found only a modest effect of familiarity on letter search, apparently because they pitted pseudowords (rather than real words) against nonwords and used lowercase rather than uppercase letters. Precuing the target letter seemed to reduce the familiarity effect they found yet further, but this conclusion is clouded by the fact that reaction time data were compared with accuracy data. Because similarity between target and nontarget letters tended to have more of an effect when familiarity had less of an effect. Massaro et al. proposed a successive model, with features being detected in the first stage and orthographic structure being used in a second stage. However, a concurrent model, with a self-terminating race between lower and higher level processes, can account for the data just as well. Data from Massaro et al. and from Krueger decisively demonstrate that there is a familiarity effect based on sequential redundancy over and above any effect based on spatial redundancy (Mason 1975). The Massaro et al. data also indicate that the relative familiarity effect is constant across various age groups (Krueger, Keen & Rublevich, 1974).

Cues↗