Studies on polynucleotides. LXXV. Specificity of tRNA for codon recognition as studied by the ribosomal binding technique.
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Amino Acid Sequence↗
SEARCH · PubMed Health
Results for “recognition code”
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Protein synthesis in rabbit reticulocytes. Factors controlling internal and terminal methionine codon recognition by the methionyl transfer ribonucleic acid species.
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Adenine Nucleotides↗
[Early recognition of idiopathic hemochromatosis with HLA-typing: use of the gene chart in man].
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Crossing Over, Genetic↗
Encoded pattern classification using constructive learning algorithms based on learning vector quantization.
A novel encoding technique is proposed for the recognition of patterns using four different techniques for training artificial neural networks (ANNs) of the Kohonen type. Each template or model pattern is overlaid on a radial grid of appropriate size, and converted to a two-dimensional feature array which then acts as the training input to the ANN. The first technique employs Kohonen's self-organizing network, each neuron of which is assigned, after training, the label of the model pattern. It is found that a graphical plot of the labels of the neurons exhibits clusters (which means in effect that the feature array pertaining to distorted versions of the same pattern belongs to a specific cluster), thereby justifying the coding strategy used in this paper. When the new, unknown pattern is input to the network, it is classified to have the same label of the neuron whose corresponding model pattern is closest to the given pattern. In an attempt to reduce the computational time and the size of the network, and simultaneously improve accuracy in recognition, Kohonen's learning vector quantization (LVQ) algorithm is used to train the ANN. To further improve the network's performance and to realize a network of minimum size, two constructive learning algorithms, both based on LVQ, are proposed: (1) multi-step learning vector quantization (MLVQ), and (2) thermal multi-step learning vector quantization (TLVQ). When the proposed algorithms are applied to the classification of noiseless and noisy (and distorted) patterns, the results demonstrate that the pattern encoding strategy and the suggested training techniques for ANNs are efficient and robust. For lack of space, only the most essential results are presented here. For details, see Ganesh Murthy and Venkatesh (1996b).
Journal Article↗
Temporal pattern sensitive and nonsensitive responses in the cat's retinal ganglion cells.
In order to characterize temporal pattern sensitivity in the cat ganglion cells, a new analysis technique by semi-Markov models which was developed in the previous papers (Tsukada et al., 1975-1977) was applied to input-output relations of the receptive-field. Three types of statistical spot stimuli positioned in the center region of receptive fields were used. Each type of stimulus has an identical histogram in the inter-stimulus intervals and therefore the same mean and variance, but different correlations between adjacent inter-stimulus intervals (Type 1, positive; Type 2, negative; and Type 3, independent processes). From the output spike trains of cat retinal ganglion cells to each stimulus, mean, variance, and histogram were computed. As the result of investigating these data, we could draw the following conclusion from the resultant output interval histograms. The receptive-field-center responses of cat ganglion cells can be classified into two groups (Types L and N) according to the difference of responsiveness to the three types of statistical spot stimuli. A Type L response has the same histogram in interspike intervals for all three stimuli, and is not sensitive to the temporal pattern, while a Type N response has three different forms depending on each type of stimulus showing high sensitivity to the temporal pattern. These results were also simulated by the Markov chain model and discussed with relation to neural coding and classification of ganglion cell types.
Animals↗
Applying Brinley plots to individuals: effects of aging on performance distributions in two speeded tasks.
This article describes the application of Brinley plots to performance distributions from 2 speeded tasks, namely, letter coding and visual search. Ss were aged either 60 years (n = 111) or 75 years (n = 111). Response times within each age group were ranked and then plotted against each other so that the best 60-year-old was paired with the best 75-year-old, and so on. For both tasks, linear fits to the functions were almost perfect, with slopes greater than 1 and with negative intercepts. Additive and multiplicative models of aging were rejected in favor of a general linear model, with different parameters for the letter coding and visual search tasks.
Aged↗
Search for letter identity and location by disabled readers.
Reading-disabled boys, reading- and age-matched controls, and adults searched letter arrays for the identity or location of a probe letter. Response time (RT) and accuracy were examined as a function of the temporal relation between probe and array letters (probe first, simultaneous, array first), and array size (1-5 letters). Although disabled readers closely resembled age controls in RT, their accuracy differed significantly when large letter arrays were tested. In the letter identification task, this was only evident when the array letters preceded the probe; in the letter location task, it occurred in all three probe conditions. Correlational analyses showed that all subjects were influenced by the visual, but not the phonological, similarity between letters. Thus, a reading-related impairment is evident in both letter identification and letter location processes, even when the phonological coding of letters has been minimized.
Adolescent↗
Encoding speed of visual features and the occurrence of illusory conjunctions.
Earlier studies have found that people show characteristic errors when asked to observe a rapid stream of events and to name the colour of a certain letter, or the letter in a certain colour. They tend to report the letter or colour from an event later in time than the correct one. This is not true, however, if they are asked to name the colour of a digit amongst letters, without knowing in advance the identity of the digit. There is also some evidence that the errors are symmetric if the location of the target is not known in advance. Three experiments are reported which show that this symmetry results from slow encoding of the colour as compared with the digit. It is still true that uncertainty about target identity does reduce the tendency to see the target in a later than an earlier colour. This effect is, however, superimposed on asymmetries resulting from coding speed, and the effect of uncertainty of location may be due only to this.
Color Perception↗
MultiPLX: automatic grouping and evaluation of PCR primers.
UNLABELLED: MultiPLX is a new program for automatic grouping of PCR primers. It can use many different parameters to estimate the compatibility of primers, such as primer-primer interactions, primer-product interactions, difference in melting temperatures, difference in product length and the risk of generating alternative products from the template. A unique feature of the MultiPLX is the ability to perform automatic grouping of large number (thousands) of primer pairs. AVAILABILITY: Binaries for Windows, Linux and Solaris are available from http://bioinfo.ebc.ee/download/. A graphical version with limited capabilities can be used through a web interface at http://bioinfo.ebc.ee/multiplx/. The source code of the program is available on request for academic users. CONTACT: maido.remm@ut.ee.
Algorithms↗
JBEAM: multiscale curve coding via beamlets.
A multiscale coder for curves and boundaries is presented. It utilizes a multiscale structure--beamlets--that is designed primarily for linear and curvilinear features. The coder is composed of three main components: 1) a rate-distortion optimized beamlet-based representation, 2) a tree-based coding from a beamlet representation to a symbol stream, and 3) an entropy coder. This coder is named "JBEAM." Taking advantage of its multiscale property, we utilized tree-based coding to make it progressive. The derived coder has a low order of computational complexity. Simulations demonstrate an advantage over the state-of-the-art industrial standard: JBIG 2. A software package, which includes an implementation of JBEAM, is made available. Variations and potential improvements of this method will be discussed. This work may inspire more activities in this line of research, improving curve coding.
Algorithms↗
Custom-built moments for edge location.
We present a general construction of functions whose moments serve to locate and parametrize step edges within an image. Previous use of moments to locate edges was limited to functions supported on a circular region, but our method allows the use of "custom-designed" functions supported on circles, rectangles, or any desired shape, and with graphs whose shape may be chosen with great freedom. We present analyses of the sensitivity of our method to pixelization errors or discrepancy between the image and an idealized edge model. The parametric edge description yielded by our method makes it especially suitable as a component of wedgelet image coding.
Algorithms↗
What you see is what you get: functional equivalence of a perceptually filled-in surface and a physically presented stimulus.
A perceptually filled-in surface, such as occurs during sustained attention to a peripheral stimulus (Troxler fading), can be functionally equivalent to a physically presented stimulus. Observers failed to detect probes that were presented in the location of a filled-in surface that had the same surface attributes as the probes; this was true even though, physically, the probes contrasted with the background. Probe stimuli with surface characteristics different from those of the filled-in surface were detected more often, though not quite as often as when there was no filled-in surface. Together, these findings support the idea that there are two components in perceptual filling: a neural filling-in component and a sustained-attention component, which actively suppresses perceptual processing at the filled-in location. More broadly, they illustrate the interplay of basic visual mechanisms in the creation and representation of visual surfaces and in the coding and detection of changes to these surfaces.
Attention↗
Spatial patterns and memory for locations.
Rats obtained food from the tops of vertical poles in a 5 x 5 matrix of locations. On each trial, the baited locations formed one of the two possible exemplars of a checkerboard spatial pattern. During training, locations that had been visited earlier in the trial were indicated by a visual cue. Following training, performance with and without the visual cues was compared. Spatial choices were controlled by the checkerboard spatial pattern. The visual cues enhanced the ability of rats to avoid revisits of locations. However, the visual cues did not enhance control by the spatial pattern, as would be expected if the same spatial memories were involved in avoidance of revisits and coding the location of baited locations.
Animals↗
Stimulus and response representations underlying orthogonal stimulus-response compatibility effects.
One of the most important findings in recent years regarding response selection is that stimulus-response compatibility (SRC) effects occur for situations in which stimulus and response sets vary along orthogonal dimensions. For two-choice tasks, two types of orthogonal SRC effects are found: an overall advantage for the up-right/down-left mapping, and mapping preferences that vary as a function of position of the response apparatus and responding hand. We review evidence regarding the nature of both types of orthogonal SRC effects. Only asymmetric coding accounts have been proposed for the up-right/down-left advantage, and the evidence indicates that this asymmetry is a property of both verbal and spatial codes. Motoric and coding accounts, as well as a hybrid account based on end-state comfort, have been proposed for the second type of orthogonal SRC effect. In this case, the effects of response-apparatus position, hand, and hand posture conform more closely to predictions of the asymmetric coding accounts than to those of the motoric accounts. We also evaluate the mechanisms proposed by the alternative accounts in terms of related literature on the properties of spatial and verbal codes. Evidence indicates that spatial information is represented in categorical and coordinate codes, and both categorical spatial codes and verbal codes are asymmetric. Experiments on mental rotation suggest that it is unlikely that the direction of rotation is determined automatically by movement constraints, as the end-state comfort hypothesis suggests. An explanation in terms of salient features and referential coding can accommodate the range of orthogonal SRC effects.
Functional Laterality↗
[A code governing specific binding of regulatory proteins to DNA and structure of stereospecific sites of regulatory proteins].
A model is proposed for the structure of stereospecific sites in regulatory proteins. On its basis a possible code is suggested that governs the binding of regulatory proteins at specific control sites on DNA. Stereospecific sites of regulatory proteins are assumed to contain pairs of antiparallel polypeptide chain segments which form a right-hand twisted antiparallel beta-sheet, with single-stranded regions at the ends of the beta-structure. The model predicts that binding reaction between a regulatory protein and double-helical DNA is a cooperative phenomenon and is accompanied by significant structural alteration at the stereospecific site of the protein. Half of hydrogen bonds normally existing in beta-structure are broken upon complex formation with DNA and a new set of hydrogen bonds is formed between polypeptide amide groups and DNA base pairs. In a stereospecific site, one chain (t-chain) is attached through hydrogen bonds to the carbonyl oxygens of pyramides and N3 adenines lying in one DNA strand, while the second polypeptide chain (g chain) is hydrogen bonded to the 2-amino groups of guanine residues lying in the opposite DNA strand. The amide groups serve as specific reaction sites being hydrogen bond acceptors in g-chain and hydrogen bond donors in t-chain. The single-stranded portions of t- and g-chains lying in neighbouring subunits of regulatory protein interact with each other forming deformed beta-sheets. The recognition of regulatory sequences by proteins is based on the structural complementarity between stereospecific sites of regulatory proteins and base pairs sequences at the control sites. An essential feature of these sequences is the asymmetrical distribution of guanine residues between the two DNA strands. The code predicts that there are six fundamental amino acid residues (serine, threonine, asparagine, histidine, glutamine and cysteine) whose sequence in stereospecific site determines the base pair sequence to which a given regulatory protein would bind preferentially. The code states a correspondence between four amino acid residues at the stereospecific site of regulatory protein with the two residues being in t- and g-segments, respectively, and AT(GC) base pair at the control site. It is thus possible to determine which amino acid residues in the repressor and which base pairs in the operator DNA are involved in specific interactions with each other, as exemplified by lac repressor binding to lac operator.
Amino Acid Sequence↗
Finding effective strategies for teaching ethics: a comparison trial of two interventions.
PURPOSE: To compare the effects of two teaching methods (written case analyses and written case analyses with group discussion) on students' recognition and assessment of common ethical dilemmas. METHOD: In 1999-2000, all third-year students at the University of Washington School of Medicine on a pediatrics clinical rotation participated in the study. Eighty students were based in Seattle and 66 were in community sites in a five-state area. All students received three scenarios with written instructions for ethical analysis, submitted written answers, and received written feedback from a single evaluator. The Seattle students also participated in an hour-long, one-time discussion group about the cases. All students submitted a final case analysis. Four components of the case analyses were evaluated: ability to identify ethical issues, see multiple viewpoints, formulate an action plan, and justify their actions. One investigator evaluated a masked subset of the case analyses from both groups to assess whether teaching method affected the students' ability to recognize and assess ethical problems. RESULTS: Forty-eight of 146 available case analysis sets (each set included three initial analyses plus one final analysis) were masked and coded. Performances on the initial analyses were similar in both groups (p >.2-.8). The discussion group had a higher absolute increase in total score (p =.017) and in ability to formulate a plan (p =.013) on the final case analysis. Performances otherwise remained largely similar. CONCLUSIONS: Students' recognition and assessment of ethical issues in pediatrics improves following a case-based exercise with structured feedback. Group discussion may optimize the learning experience and increase students' satisfaction.
Clinical Clerkship↗
AM representation in green treefrog auditory nerve fibers: neuroethological implications for pattern recognition and sound localization.
In addition to spectral call components, temporal patterns in the advertisement-call envelope of green treefrog males ( Hyla cinerea) provide important cues for female mate choice. Rapid amplitude modulation (AM) with rates of 250-300 Hz is typical for this species' advertisement calls. Here we report data on the encoding of these rapid call modulations by studying the responses of single auditory nerve fibers to two-tone stimuli with envelope periodicities close to those of the natural call. The free-field response properties of 86 nerve fibers were studied from 32 anesthetized males. The accuracy of stimulus envelope coding was quantified using both a Gaussian function fit to the interspike interval histograms derived from the first seven 20-ms stimulus segments, and the vector-strength metric applied to the phase-locked responses. Often, AM encoding in the initial stimulus segment was more faithful than that in its second half. This result may explain why conspecific females prefer calls in which the initial segment is unmasked rather than masked. Both the questions of pattern recognition and localization are discussed, and the data are related to behavioral observations of female choice and localization performance in this species.
Acoustic Stimulation↗
Primary structure of the mannose receptor contains multiple motifs resembling carbohydrate-recognition domains.
Macrophages express a cell surface receptor which mediates phagocytosis and pinocytosis of particles and solutes containing mannose (fucose and N-acetylglucosamine are also ligands for the receptor). An apparently identical protein has been isolated from human placenta. Proteolytic fragments of the placental receptor were sequenced so that oligonucleotide probes complementary to the receptor cDNA could be generated. These probes were used to isolate cDNA clones covering the entire coding portion of the mRNA for the receptor. Confirmation that these clones encode the mannose receptor was obtained by expression in rat fibroblasts. The expressed protein mediates uptake and degradation of mannose-conjugated serum albumin. The deduced amino acid sequence of the receptor reveals that it is most likely to be a type I transmembrane protein (COOH terminus on the cytoplasmic side of the membrane) since the mature polypeptide is preceded by a signal sequence and a hydrophobic stop transfer sequence is located 45 amino acids from the COOH terminus. The extracellular portion of the receptor polypeptide consists of three types of domains. The first 139 amino acids constitute a cysteine-rich segment which does not resemble other known sequences. There follows a domain which closely resembles fibronectin type II repeats. The remainder of the extracellular portion of the receptor is composed of eight segments homologous with the C-type carbohydrate-recognition domains of the asialoglycoprotein receptor, mannose binding proteins, and other Ca2(+)-dependent animal lectins. This structure suggests that the receptor may contain multiple ligand-binding domains thus accounting for its tight binding to highly multivalent ligands.
Amino Acid Sequence↗
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