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Color constancy at a pixel.

In computational terms we can solve the color constancy problem if device red, green, and blue sensor responses, or RGB's, for surfaces seen under an unknown illuminant can be mapped to corresponding RGB's under a known reference light. In recent years almost all authors have argued that this three-dimensional problem is too hard. It is argued that because a bright light striking a dark surface results in the same physical spectra as those of a dim light incident on a light surface, the magnitude of RGB's cannot be recovered. Consequently, modern color constancy algorithms attempt only to recover image chromaticities under the reference light: They solve a two-dimensional problem. While significant progress has been made toward achieving chromaticity constancy, recent work has shown that the most advanced algorithms are unable to render chromaticity stable enough so that it can be used as a cue for object recognition [B. V. Funt, K. Bernard, and L. Martin, in Proceedings of the Fifth European Conference on Computer Vision (European Vision Society, Springer-Verlag, Berlin, 1998), Vol. II, p. 445.] We take this reductionist approach a little further and look at the one-dimensional color constancy problem. We ask, Is there a single color coordinate, a function of image chromaticities, for which the color constancy problem can be solved? Our answer is an emphatic yes. We show that there exists a single invariant color coordinate, a function of R, G, and B, that depends only on surface reflectance. Two corollaries follow. First, given an RGB image of a scene viewed under any illuminant, we can trivially synthesize the same gray-scale image (we simply code the invariant coordinate as a gray scale). Second, this result implies that we can solve the one-dimensional color constancy problem at a pixel (in scenes with no color diversity whatsoever). We present experiments that show that invariant gray-scale histograms are a stable feature for object recognition. Indexing on invariant distributions supports almost perfect recognition for a dataset of 11 objects viewed under five colored lights. In contrast, object recognition based on chromaticity histograms (post-color constancy preprocessing) delivers much poorer recognition.

Artificial Intelligence↗

Presence of ghost doublets of coded neuronal patterns: relation to synaptic memory storage.

Recent evidence demonstrates that controlled visual stimuli cause the generation, in the primary visual cortex of rhesus monkey cells, of large numbers of very precisely replicating copies of complex patterns of discharge consisting of three or more spikes, the patterns of which presumedly code for specific qualities of the stimuli presented. We present evidence that the copies of precisely replicating triplets of spikes, generally not exceeding 100 ms in duration, occur in close time proximity to many copies of highly precise "ghost" doublets. These doublets are defined as patterns consisting of two pulses, with precise separations in time, specifically those that would be generated if any one of the pulses making up a given replicating triplet were missing. In striking contrast, nonreplicating triplets (also present in these records)--that is, triplets made up of intervals that are not present in replicating triplets--are not accompanied by such ghost doublets. The persistence (memory) of capacity to produce such ghost doublets decays according to two independent kinetic rules. The first of these results in the disappearance of such doublets within about 0.1 s as measured by two independent methods, whereas the second disappears only after several minutes or longer. These results provide strong evidence consistent with the notion that at least some parts of the brain transmit, store representations of, and retrieve qualitative information through the use of a code consisting of specific patterns of nerve discharges in time.

Animals↗

Artiodactyl emergence is accompanied by the birth of an extensive pool of diverse germline TRDV1 genes.

Molecular cloning of cDNA from gamma/delta T cells has shown that in sheep, the variable domain of the delta chain is chiefly determined by the expression of the TRDV1 subgroup, apparently composed of a large number of genes. There are three other TRDV subgroups, but these include only one gene each. To evaluate the extent and the complexity of the genomic TRDV repertoire, we screened a sheep liver genomic library from a single individual of the Altamurana breed and sheep fibroblast genomic DNA from a single individual of the Gentile di Puglia breed. We identified a total of 22 TRDV1 genes and the TRDV4 gene. A sequence comparison between germline and the rearranged genes indicates that, in sheep, the TRDV repertoire is generated by the VDJ rearrangement of at least 40 distinct TRDV1 genes. All germline TRDV1 genes present a high degree of similarity in their coding as well as in 5' and 3' flanking regions. However, a systematic analysis of the translation products reveals that these genes present a broadly different and specific repertoire in the complementarity-determining regions or recognition loops, allowing us to organize the TRDV genes into sets. We assume that selection processes operating at the level of ligand recognition have shaped the sheep TRDV germline repertoire. A phylogenetic study based on a sequence analysis of the TRDV genes from different mammalian species shows that the diversification level of these genes is higher in artiodactyl species compared to humans and mice.

Amino Acid Sequence↗

Target--distractor separation and feature integration in visual attention to letters.

The interference produced by distractor letters diminishes with increasing distance from a target letter, as if the distractors fall outside an attentional spotlight focussed on the target (Eriksen and Eriksen 1974). We examine Hagenaar and Van der Heijden's (1986) claim that this distance effect is an acuity artefact. Feature integration theory (Treisman 1986) predicts that even when acuity is controlled for, distance effects should be found when interference is produced by conjoined distractor features (e.g. letter-identities), but not when interference arises from isolated distractor features (e.g. letter-strokes). The opposite pattern of results is found. A model is proposed in which both letter-strokes and letter-identities are derived in parallel. The location of letter-strokes can also be coded in parallel, but locating letter-identities may require the operation of attention.

Attention↗

Regional autonomy in the peripheral processing of odor signals in newborn rabbits.

In newborn rabbits, small and apparently arbitrary regions of the olfactory bulb and associated epithelium appear capable of a high degree of odor processing. After medial or lateral removal of up to 80% of the olfactory bulbs, including the accessory bulb, newborn pups were still able to respond appropriately to the pheromone-governing suckling behavior (Expt. I), could rapidly learn to associate a novel, artificial odor with suckling (Expt. II), and continued to respond appropriately to artificial odors learned prior to lesioning (Expt. III). These findings suggest that the perception and recognition of such suckling signals does not depend on the integration of information from the entire bulb or epithelium, and question the extent to which patterns of 2-deoxyglucose uptake in the bulb reflect the neural coding for specific odors. However, as the tasks set here only required detection of odor signals and not true odor discrimination, it may still be that the full bulbar pattern of activation is necessary for higher-order processing, such as distinguishing between odors and attributing different meanings to them.

Animals↗

Exon prediction in eucaryotic genomes.

Two independent computer systems, NetPlantGene and AMELIE, dedicated to the identification of splice sites in plant and human genomes, respectively, are introduced here. Both methods were designed in relation to experimental work; they rely on automatically generated rules involving the nucleotide content of sequences regardless of the coding properties of exons. The specificity of plant sequences as considered in NetPlantGene is shown to enhance the quality of detection as opposed to general methods such as GRAIL. A scanning model of the acceptor site recognition is being simulated by AMELIE leading to a relatively accurate selection process of sites.

Arabidopsis↗

Analysis of sequential letter matching tasks utilising lateralised tachistoscopic presentation.

Four experiments are reported in which sequential matches were demanded for double letter stimuli, the first stimulus pair was presented in central vision and the second in the left or right field. The responses were analysed according to the type of classification required (physical or nominal identify, or different). The results indicated that there were alterations in laterality patterns between retention intervals of 50 msec. and 990 msec. despite evidence for a prolonged and stable form of visual memory. These findings were incompatible with a model of the letter matching task which maps "name" codes to the left hemisphere and "visual" codes to the right.

Dominance, Cerebral↗

A new method to detect related function among proteins independent of sequence and fold homology.

A new method has been developed to detect functional relationships among proteins independent of a given sequence or fold homology. It is based on the idea that protein function is intimately related to the recognition and subsequent response to the binding of a substrate or an endogenous ligand in a well-characterized binding pocket. Thus, recognition of similar ligands, supposedly linked to similar function, requires conserved recognition features exposed in terms of common physicochemical interaction properties via the functional groups of the residues flanking a particular binding cavity. Following a technique commonly used in the comparison of small molecule ligands, generic pseudocenters coding for possible interaction properties were assigned for a large sample set of cavities extracted from the entire PDB and stored in the database Cavbase. Using a particular query cavity a series of related cavities of decreasing similarity is detected based on a clique detection algorithm. The detected similarity is ranked according to property-based surface patches shared in common by the different clique solutions. The approach either retrieves protein cavities accommodating the same (e.g. co-factors) or closely related ligands or it extracts proteins exhibiting similar function in terms of a related catalytic mechanism. Finally the new method has strong potential to suggest alternative molecular skeletons in de novo design. The retrieval of molecular building blocks accommodated in a particular sub-pocket that shares similarity with the pocket in a protein studied by drug design can inspire the discovery of novel ligands.

Algorithms↗

Role of the international organisation for animal health (Office International des Epizooties: OIE) in the control of foot and mouth disease.

The author describes activities conducted by the International Organisation for Animal Health (OIE: Office International des Epizooties) to control foot and mouth disease (FMD) world-wide. These activities fall within the framework of the principal missions of the OIE. The first of these missions is the collection and dissemination of epidemiological information and of scientific knowledge on animal diseases, the socio-economic or disease implications of which can be particularly serious. The implementation of the measures required to control the disease and to protect countries threatened by FMD depends on the quality and rapidity of the transmission of this information. The co-ordination of studies, research and control programmes against FMD is equally important for the OIE. This work is based, in particular, on work conducted by the OlE foot and mouth disease and other epizootics Commission. OIE Member Countries not only have access to the most recent data on the diagnosis, surveillance and control of FMD but also have recourse to the official recognition procedure for disease-free status provided by this Commission. Finally, through the standardisation of health recommendations, diagnostic tests, manufacture protocols and the control of biological products, made available by the OIE International Animal Health Code Commission in regard to the former and by the OIE Standards Commission in regard to the latter, the OIE provides the reference for international trade in animals and animal products, and is recognised in this role by the World Trade Organization.

Animal Welfare↗

Ambiguous coding is required for the lethal interaction between methylated DNA bases and DNA mismatch repair.

The thiopurine 6-thioguanine (S6G) is used to treat acute leukaemia. Its cytotoxic effect requires an active DNA mismatch repair (MMR) system. S6G is incorporated into DNA where a small fraction undergoes in situ conversion to S6-thiomethylguanine (S6meG). After replication, S6meG-containing base pairs interact with MMR. This interaction is ultimately lethal and MMR-defective cells are resistant to S6G. Here, we report that growing human cells extensively incorporate the thiopyrimidine nucleoside 4-thiothymidine (S4TdR) into their DNA. The incorporated thiopyrimidine (S4T) can also undergo facile S-methylation to 4-thiomethylthymine (S4meT). The rate of methylation of S4TdR in model substrates is similar to that for the conversion of S6G to S6meG indicating that the DNA of cells grown in S4TdR will contain significant levels of S4meT. Despite this, S4TdR is not associated with MMR-related cell death. We demonstrate that, in contrast to S6meG, neither DNA S4T nor S4meT codes ambiguously. S4T retains the coding properties of unmodified T, whereas S4meT behaves like a normal cytosine and exclusively directs the incorporation of guanine. The preferred S4meT:G base pair is also a poor substrate for binding by the hMutSalpha mismatch recognition factor. We suggest that the ability of S4meT to produce a structurally acceptable base pair during replication underlies the absence of MMR-related death in cells treated with S4TdR.

Base Pair Mismatch↗

Isolation of a human cDNA for alpha 2-thiol proteinase inhibitor and its identity with low molecular weight kininogen.

A lambda gt11 cDNA library containing DNA inserts prepared from human liver mRNA has been screened with an antibody to human alpha 2-thiol proteinase inhibitor that was isolated from fresh plasma. Eighteen positive clones were isolated from one million phage, and each was plaque purified. The cDNA insert of one of these phage was sequenced and shown to code for alpha 2-thiol proteinase inhibitor as identified by a partial amino acid sequence of the light chain of alpha 2-thiol proteinase inhibitor. This cDNA insert contained 1529 base pairs coding for the complete alpha 2-thiol proteinase inhibitor. It included 45 base pairs of 5' noncoding sequence, 1281 base pairs that code for pre alpha 2-thiol proteinase inhibitor, a stop codon, 160 base pairs of 3' noncoding sequence, and 40 base pairs of poly(A) tail. The noncoding sequence on the 3' end contained a potential recognition site (AATAAA) for processing and polyadenylation of precursor messenger RNA. The amino acid sequence of alpha 2-thiol proteinase inhibitor deduced from the cDNA showed a striking similarity (overall homology at 74%) to that of bovine low molecular weight (LMW) kininogen, including two internally repeated sequences and a nonapeptide sequence of bradykinin. These data clearly indicated that alpha 2-thiol proteinase inhibitor and LMW kininogen are identical. This was further supported by immunological cross-reactivity between alpha 2-thiol proteinase inhibitor and LMW kininogen.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Processing of visually presented clock times.

The encoding and representation of visually presented clock times was investigated in three experiments utilizing a comparative judgment task. Experiment 1 explored the effects of comparing times presented in different formats (clock face, digit, or word), and Experiment 2 examined angular distance effects created by varying positions of the hands on clock faces. In Experiment 3, encoding and processing differences between clock faces and digitally presented times were directly measured. Same/different reactions to digitally presented times were faster than to times presented on a clock face, and this format effect was found to be a result of differences in processing that occurred after encoding. Angular separation also had a limited effect on processing. The findings are interpreted within the framework of theories that refer to the importance of representational codes. The applicability to the data of Bank's semantic-coding theory, Paivio's dual-coding theory, and the levels-of-processing view of memory are discussed.

Discrimination Learning↗

Electrophysiological evidence for temporal overlap among contingent mental processes.

A series of studies assessed perceptual-motor transmission of stimulus information by measuring lateralization of movement-related brain potentials in a choice reaction task with no-go trials. When stimuli varied in shape and size, lateralized potentials on no-go trials suggested that easily recognized shape information was used to initiate motor preparation and that this preparation was aborted when size analysis signified that the response should be withheld. This indicates that movement preparation can begin once partial perceptual information about a stimulus becomes available, contrary to an assumption of fully discrete models of information processing. By contrast, when stimuli varied only in size, no evidence for preliminary response preparation was obtained, contrary to an assumption of fully continuous models but consistent with asynchronous discrete coding models (Miller, 1982, 1988).

Adult↗

Awareness and understanding of dementia in African/Caribbean and South Asian families.

The objective of this study was to explore awareness, recognition and understanding of dementia symptoms in families of South Asian and African/Caribbean descent in the UK. In-depth, semistructured interviews were carried out with South Asian and African/Caribbean carers. Interview transcripts were analysed by coding the data into themes and investigating links between them, using the constant comparison approach of grounded theory. Thirty carers of a person with dementia of South Asian and African/Caribbean heritage were interviewed. Maximum variation sampling was used to include carers with a broad range of socio-demographic characteristics. Most participants were aware of the condition "dementia", but used different terms to describe the disorder. Many, however, had not heard of the condition before their relative developed it, suggesting general awareness of dementia is low. Difficulties can arise in the caring relationship due to a lack of understanding of the condition--in particular when family members place blame for the symptoms on the person with dementia. Conclusions of the study are that knowledge of dementia is limited, in terms of awareness of the condition as well as understanding of the causes. This research highlights the importance of raising dementia awareness and emphasises the importance of the provision of clear and understandable information, from health and social service providers.

Adult↗

Oncogene-related serum proteins and cancer risk: a nested case-control study.

Proto-oncogenes are genes coding for factors involved in cellular growth, reproduction, and differentiation. Cancer results through mutations of proto-oncogenes or through other mechanisms involving the products of proto-oncogenes. This study asks whether serum proteins immunologically related to the products of proto-oncogenes distinguish older men and women who manifest a new cancer during a 2-year follow-up. The authors conducted a nested case-control study that involved 248 men and women selected from a larger group of older (age > or = 65 years) healthy volunteers in a randomized clinical trial of preventive clinical services. Study subjects included 37 with a fatal cancer, 59 non-fatal breast, prostate, colon, or lung cancer, 58 hospitalized with at least one discharge diagnosis that coded to benign neoplasia (International Classification of Diseases, 9th Revision codes 210-239), and 94 randomly selected controls. Using seven monoclonal antibodies prepared against ras, erb-B, FES, myb, and SIS polypeptide sequences, immunoblots detected 17 proteins in serum collected from subjects before the clinical recognition of cancer. Five oncogene-related serum proteins appeared to distinguish older persons who manifested fatal (but not non-fatal) cancer over a brief (2-year) follow-up. Older persons hospitalized with benign neoplasia also had higher levels of these serum proteins. Relative to the 94 control subjects, a 52,000 dalton SIS-related protein (odd ratio (OR) = 5.9, 95% confidence interval (CI) 1.4-24.9) and a 35,000 dalton k-ras-related protein (OR = 11.3, 95% CI 1.2-104) were particularly common in serum from the 37 subjects who manifested a fatal cancer.

Aged↗

Ataxia-telangiectasia locus: sequence analysis of 184 kb of human genomic DNA containing the entire ATM gene.

Ataxia-telangiectasia (A-T) is an autosomal recessive disorder involving cerebellar degeneration, immunodeficiency, chromosomal instability, radiosensitivity, and cancer predisposition. The genomic organization of the A-T gene, designated ATM, was established recently. To date, more than 100 A-T-associated mutations have been reported in the ATM gene that do not support the existence of one or several mutational hotspots. To allow genotype/phenotype correlations it will be important to find additional ATM mutations. The nature and location of the mutations will also provide insights into the molecular processes that underly the disease. To facilitate the search for ATM mutations and to establish the basis for the identification of transcriptional regulatory elements, we have sequenced and report here 184,490 bp of genomic sequence from the human 11q22-23 chromosomal region containing the entire ATM gene, spanning 146 kb, and 10 kb of the 5'-region of an adjacent gene named E14/NPAT. The latter shares a bidirectional promoter with ATM and is transcribed in the opposite direction. The entire region is transcribed to approximately 85% and translated to 5%. Genome-wide repeats were found to constitute 37.2%, with LINE (17.1%) and Alu (14.6%) being the main repetitive elements. The high representation of LINE repeats is attributable to the presence of three full-length LINE-1s, inserted in the same orientation in introns 18 and 63 as well as downstream of the ATM gene. Homology searches suggest that ATM exon 2 could have derived from a mammalian interspersed repeat (MIR). Promoter recognition algorithms identified divergent promoter elements within the CpG island, which lies between the ATM and E14/NPAT genes, and provide evidence for a putative second ATM promoter located within intron 3, immediately upstream of the first coding exon. The low G+C level (38.1%) of the ATM locus is reflected in a strongly biased codon and amino acid usage of the gene.

Ataxia Telangiectasia↗

Molecular cloning of preproacrosin and analysis of its expression pattern in spermatogenesis.

Complementary DNA clones for the boar preproacrosin have been isolated from a randomly primed testis cDNA library in lambda gt10 and from an oligo(dT)-primed testis cDNA in lambda gt11. The nucleotide sequence of the 1418-bp cDNA insert includes a 46-bp 5'-untranslated region, an open reading frame of 1248 bp corresponding to 416 amino acids (45.59 kDa) and a 121-bp 3'-untranslated region. The deduced amino acid sequence includes the active-site residues histidine, asparagine and serine of the catalytic triad of the serine proteinase super-family and is colinear with that determined by amino acid sequencing of the boar acrosin light chain and of a small region of the NH2-terminal sequence of the heavy chain. The preproacrosin cDNA contains at the 3' end a 381-bp sequence which codes for an amino acid sequence not yet found in any other serine proteinase. This amino acid sequence is rich in proline (42 out of 127 amino acids) and is suggested to be involved in the recognition and binding of the spermatozoa to the zona pellucida of the ovum. The mRNA for preproacrosin is synthesized as an approximately 1.6-kb-long molecule only in the postmeiotic stages of boar and bull spermatogenesis.

Acrosin↗

Anaerobic regulation of transcription initiation in the arcDABC operon of Pseudomonas aeruginosa.

The arcDABC operon of Pseudomonas aeruginosa encodes the enzymes of the arginine deiminase pathway, which is inducible under conditions of oxygen limitation and serves to generate ATP from arginine. The 5' end of arc mRNA extracted from anaerobically grown cells was determined by S1 and primer extension mapping. The transcription initiation site was located upstream of the arcD gene and 41.5 bp downstream of the center of the sequence TTGAC....ATCAG. This sequence, termed the ANR box, is similar to the consensus FNR recognition site of Escherichia coli. Transcription of the arc operon in P. aeruginosa was strongly decreased by a deletion of the TTGAC half site or by a mutation in the anr gene, which is known to code for the FNR-like regulatory protein ANR. During a transition from aerobic to anaerobic growth conditions, the concentrations of arc mRNAs and the levels of the ArcD and ArcA proteins rose in a parallel fashion. Mutational analysis of the arc promoter region led to the conclusion that the distance between the ANR box and the -10 promoter region is important for promoter strength, whereas the -35 region does not appear to be critical for arc promoter function. These findings and previous results indicate that anaerobic induction of the arc operon occurs at the level of transcription and requires the ANR box in cis and the ANR protein in trans.

Amino Acid Sequence↗