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PubMed1989

Primary structure of rat brain prostaglandin D synthetase deduced from cDNA sequence.

The amino acid sequence of rat brain prostaglandin D synthetase (Urade, Y., Fujimoto, N., and Hayaishi, O. (1985) J. Biol. Chem. 260, 12410-12415) was determined by a combination of cDNA and protein sequencing. cDNA clones specific for this enzyme were isolated from a lambda gt11 rat brain cDNA expression library. Nucleotide sequence analyses of cloned cDNA inserts revealed that this enzyme consisted of a 564- or 549-base pair open reading frame coding for a 188- or 183-amino acid polypeptide with a Mr of 21,232 or 20,749 starting at the first or second ATG. About 60% of the deduced amino acid sequence was confirmed by partial amino acid sequencing of tryptic peptides of the purified enzyme. The recognition sequence for N-glycosylation was seen at two positions of amino acid residues 51-53 (-Asn-Ser-Ser-) and 78-80 (-Asn-Leu-Thr-) counted from the first Met. Both sites were considered to be glycosylated with carbohydrate chains of Mr 3,000, since two smaller proteins with Mr 23,000 and 20,000 were found during deglycosylation of the purified enzyme (Mr 26,000) with N-glycanase. The prostaglandin D synthetase activity was detected in fusion proteins obtained from lysogens with recombinants coding from 34 and 19 nucleotides upstream and 47 and 77 downstream from the first ATG, indicating that the glycosyl chain and about 20 amino acid residues of N terminus were not essential for the enzyme activity. The amino acid composition of the purified enzyme indicated that about 20 residues of hydrophobic amino acids of the N terminus are post-translationally deleted, probably as a signal peptide. These results, together with the immunocytochemical localization of this enzyme to rough-surfaced endoplasmic reticulum and other nuclear membrane of oligodendrocytes (Urade, Y., Fujimoto, N., Kaneko, T., Konishi, A., Mizuno, N., and Hayaishi, O. (1987) J. Biol. Chem. 262, 15132-15136) suggest that this enzyme is a membrane-associated protein.

Amino Acid Sequence↗
PubMed1982

Children's memory for recurring linguistic and nonlinguistic material in relation to reading ability.

Good beginning readers typically surpass poor beginning readers in memory for linguistic material such as syllables, words, and sentences. Here we present evidence that this interaction between reading ability and memory performance does not extend to memory for nonlinguistic material like faces and nonsense designs. Using an adaptation of the continuous recognition memory paradigm of Kimura (1963) we assessed the ability of good and poor readers in the second grade to remember three different types of material: photographs of unfamiliar faces, nonsense designs, and printed nonsense syllables. For both faces and designs, the performance of the two reading groups was comparable; only when remembering the nonsense syllables did the good readers perform at a significantly superior level. These results support other evidence that distinctions between good and poor beginning readers do not turn on memory, per se, but rather on memory for linguistic material. Thus they extend our previous finding that poor readers encounter specific difficulty with the use of linguistic coding in short-term memory.

Child↗
PubMed1999

Significantly lower entropy estimates for natural DNA sequences.

If DNA were a random string over its alphabet {A, C, G, T}, an optimal code would assign two bits to each nucleotide. DNA may be imagined to be a highly ordered, purposeful molecule, and one might therefore reasonably expect statistical models of its string representation to produce much lower entropy estimates. Surprisingly, this has not been the case for many natural DNA sequences, including portions of the human genome. We introduce a new statistical model (compression algorithm), the strongest reported to date, for naturally occurring DNA sequences. Conventional techniques code a nucleotide using only slightly fewer bits (1.90) than one obtains by relying only on the frequency statistics of individual nucleotides (1.95). Our method in some cases increases this gap by more than fivefold (1.66) and may lead to better performance in microbiological pattern recognition applications. One of our main contributions, and the principle source of these improvements, is the formal inclusion of inexact match information in the model. The existence of matches at various distances forms a panel of experts which are then combined into a single prediction. The structure of this combination is novel and its parameters are learned using Expectation Maximization (EM). Experiments are reported using a wide variety of DNA sequences and compared whenever possible with earlier work. Four reasonable notions for the string distance function used to identify near matches, are implemented and experimentally compared. We also report lower entropy estimates for coding regions extracted from a large collection of nonredundant human genes. The conventional estimate is 1.92 bits. Our model produces only slightly better results (1.91 bits) when considering nucleotides, but achieves 1.84-1.87 bits when the prediction problem is divided into two stages: (i) predict the next amino acid-based on inexact polypeptide matches, and (ii) predict the particular codon. Our results suggest that matches at the amino acid level play some role, but a small one, in determining the statistical structure of nonredundant coding sequences.

Algorithms↗
PubMed2007

Priming reveals differential coding of symbolic and non-symbolic quantities.

Number processing is characterized by the distance and the size effect, but symbolic numbers exhibit smaller effects than non-symbolic numerosities. The difference between symbolic and non-symbolic processing can either be explained by a different kind of underlying representation or by parametric differences within the same type of underlying representation. We performed a primed naming study to investigate this issue. Prime and target format were manipulated (digits or collections of dots) as well as the numerical distance between prime and target value. Qualitatively different priming patterns were observed for the two formats, showing that the underlying representations differed in kind: Digits activated mental number representations of the place coding type, while collections of dots activated number representations of the summation coding type.

Adult↗
PubMed1990

Role of spatial location in integration of pictorial information across saccades.

Identification of a fixated object in a visual display is facilitated by integrating information from a preview of that object in the periphery with information extracted on the subsequent foveal fixation (Pollatsek, Rayner, & Collins, 1984). These experiments investigated the extent to which this integration is dependent on the spatial location of the information remaining constant. Two preview objects were presented in the periphery; Ss fixated that region and named a single target object that appeared in the same spatial location in which one of the two preview objects had been presented. Of primary interest was the facilitative effect when a preview object was identical to the target object as a function of whether they were in the same spatial location. The major finding was that although there was a small effect of switching, there was still a substantial preview benefit even when the location of the identical object switched. In addition, the switching effect did not interact with the level of identity between the preview and target. There was also a preview benefit in conditions in which there were no eye movements and the preview and target objects were at least 5 degrees apart. Thus, the data indicate that the process object identification is relatively insensitive to location information and that object information and location information are coded fairly independently.

Adult↗
PubMed1991

A generic algorithm for finding restriction sites within DNA sequences.

This paper describes a generic algorithm for finding restriction sites within DNA sequences. The 'genericity' of the algorithm is made possible through the use of set theory. Basic elements of DNA sequences, i.e. nucleotides (bases), are represented in sets, and DNA sequences, whether specific, ambiguous or even protein-coding, are represented as sequences of those sets. The set intersection operation demonstrates its ability to perform pattern-matching correctly on various DNA sequences. The performance analysis showed that the degree of complexity of the pattern matching is reduced from exponential to linear. An example is given to show the actual and potential restriction sites, derived by the generic algorithm, in the DNA sequence template coding for a synthetic calmodulin.

Algorithms↗
PubMed2004

Simultaneous search for multiple QTL using the global optimization algorithm DIRECT.

MOTIVATION: A simultaneous search is necessary for maximizing the power to detect epistatic quantitative trait loci (QTL). The computational complexity demands that the traditional exhaustive search be replaced by a more efficient global optimization algorithm. RESULTS: We have the previously known algorithm adapted DIRECT, to the problem of simultaneous mapping of multiple QTL. We have compared DIRECT with standard exhaustive search and a genetic algorithm previously used for QTL mapping in two dimensions. In all two- and three-QTL test cases, DIRECT accurately finds the global optimum two to four orders of magnitude faster than when using an exhaustive search, and one order of magnitude faster than when using the genetic algorithm. Thus, randomization testing for determining empirical significance thresholds for at least three QTL is made feasible by the use of DIRECT. AVAILABILITY: The code of the prototype implementation is available at http://user.it.uu.se/~kl/qtl_software.html

Algorithms↗
PubMed2004

Context modeling based on context quantization with application in wavelet image coding.

Context modeling is widely used in image coding to improve the compression performance. However, with no special treatment, the expected compression gain will be cancelled by the model cost introduced by high order context models. Context quantization is an efficient method to deal with this problem. In this paper, we analyze the general context quantization problem in detail and show that context quantization is similar to a common vector quantization problem. If a suitable distortion measure is defined, the optimal context quantizer can be designed by a Lloyd style iterative algorithm. This context quantization strategy is applied to an embedded wavelet coding scheme in which the significance map symbols and sign symbols are directly coded by arithmetic coding with context models designed by the proposed quantization algorithm. Good coding performance is achieved.

Algorithms↗
PubMed2003

Modulation by context of a scene in monkey anterior inferotemporal cortex during a saccadic eye movement task.

We investigated the effect of a scene on the activity of cells in the anterior inferotemporal (AIT) cortex while the monkey performed a saccadic eye movement (SEM) task with and without the context of a scene (gray frame). Most neurons did not code for the presence of a scene when it appeared alone (monkey free viewing) or when the monkey was fixating. Nevertheless, when a peripheral target was turned on and the monkey had to make a SEM to it, some cells were capable of differentially coding the presence of the scene before and after the saccade.

Animals↗
PubMed1998

Repressor elements in the coding region of the human histone H4 gene interact with the transcription factor CDP/cut.

The coding region of the human histone H4 gene FO108 undergoes dynamic changes in chromatin structure that correlate with modifications in gene expression. Such structural alterations generally reflect transcription factor interactions with gene regulatory sequences. To test for regulatory elements within the coding region, we performed transient transfection experiments in HeLa cells using constructs with histone H4 sequences fused upstream of a heterologous thymidine kinase promoter and CAT reporter gene. H4 gene sequences from -10 to +210 repressed transcription 4.8-fold. Further deletion and mutational analysis delineated three repressor elements within this region. Using oligonucleotide competition analysis and specific antibody recognition in electrophoretic mobility shift assays, as well as methylation interference and DNase I footprinting analyses, we have identified the CCAAT displacement protein (CDP/cut) as the factor that interacts with these three repressor elements. CDP/cut binding to these repressor sites is proliferation-specific and cell-cycle-regulated, increasing in mid to late S phase. Our results indicate that the proximal 200 nucleotides of the histone H4-coding region contain transcriptional regulatory elements that may contribute to cell-cycle control of histone gene expression by interacting with repressor complexes containing CDP/cut homeodomain transcription factors.

Base Sequence↗
PubMed1986

Nucleotide sequence and characteristics of the gene for L-lactate dehydrogenase of Thermus caldophilus GK24 and the deduced amino-acid sequence of the enzyme.

The gene for L-lactate dehydrogenase (LDH) (EC 1.1.1.27) of Thermus caldophilus GK24 was cloned in Escherichia coli using synthetic oligonucleotides as hybridization probes. The nucleotide sequence of the cloned DNA was determined. The primary structure of the LDH was deduced from the nucleotide sequence. The deduced amino acid sequence agreed with the NH2-terminal and COOH-terminal sequences previously reported and the determined amino acid sequences of the peptides obtained from trypsin-digested T. caldophilus LDH. The LDH comprised 310 amino acid residues and its molecular mass was determined to be 32,808. On alignment of the whole amino acid sequences, the T. caldophilus LDH showed about 40% identity with the Bacillus stearothermophilus, Lactobacillus casei and dogfish muscle LDHs. The T. caldophilus LDH gene was expressed with the E. coli lac promoter in E. coli, which resulted in the production of the thermophilic LDH. The gene for the T. caldophilus LDH showed more than 40% identity with those for the human and mouse muscle LDHs on alignment of the whole nucleotide sequences. The G + C content of the coding region for the T. caldophilus LDH was 74.1%, which was higher than that of the chromosomal DNA (67.2%). The G + C contents in the first, second and third positions of the codons used were 77.7%, 48.1% and 95.5% respectively. The high G + C content in the third base caused extremely non-random codon usage in the LDH gene. About half (48.7%) the codons in the LDH gene started with G, and hence there were relatively high contents of Val, Ala, Glu and Gly in the LDH. The contents of Pro, Arg, Ala and Gly, which have high G + C contents in their codons, were also high. Rare codons with U or A as the third base were sometimes used to avoid the TCGA sequence, the recognition site for the restriction endonuclease, TaqI. Two TCGA sequences were found only in the sequence of CTCGAG (XhoI site) in the sequenced region of the T. caldophilus DNA. There were three segments with similar sequences in the two 5' non-coding regions, probably the promoter and ribosome-binding regions, of the genes for the T. caldophilus LDH and the Thermus thermophilus 3-isopropylmalate dehydrogenase.

Amino Acid Sequence↗
PubMed2006

Letter position information and printed word perception: the relative-position priming constraint.

Six experiments apply the masked priming paradigm to investigate how letter position information is computed during printed word perception. Primes formed by a subset of the target's letters facilitated target recognition as long as the relative position of letters was respected across prime and target (e.g., "arict" vs. "acirt" as primes for the target "apricot"). Priming effects were not influenced by whether or not absolute, length-dependent position was respected (e.g., "a-ric-t" vs. "arict"/"ar-i-ct"). Position of overlap of relative-position primes (e.g., apric-apricot; ricot-apricot; arict-apricot) was found to have little influence on the size of priming effects, particularly in conditions (i.e., 33 ms prime durations) where there was no evidence for phonological priming. The results constrain possible schemes for letter position coding.

Attention↗
PubMed2005

Learning viewpoint invariant object representations using a temporal coherence principle.

Invariant object recognition is arguably one of the major challenges for contemporary machine vision systems. In contrast, the mammalian visual system performs this task virtually effortlessly. How can we exploit our knowledge on the biological system to improve artificial systems? Our understanding of the mammalian early visual system has been augmented by the discovery that general coding principles could explain many aspects of neuronal response properties. How can such schemes be transferred to system level performance? In the present study we train cells on a particular variant of the general principle of temporal coherence, the "stability" objective. These cells are trained on unlabeled real-world images without a teaching signal. We show that after training, the cells form a representation that is largely independent of the viewpoint from which the stimulus is looked at. This finding includes generalization to previously unseen viewpoints. The achieved representation is better suited for view-point invariant object classification than the cells' input patterns. This property to facilitate view-point invariant classification is maintained even if training and classification take place in the presence of an--also unlabeled--distractor object. In summary, here we show that unsupervised learning using a general coding principle facilitates the classification of real-world objects, that are not segmented from the background and undergo complex, non-isomorphic, transformations.

Action Potentials↗
PubMed1992

Towards an exemplar model of face processing: the effects of race and distinctiveness.

Valentine (1991a, 1991b) described a theoretical framework for face recognition in which faces are encoded as locations in a multidimensional space. It was argued that this approach could provide a unified account of the effects of distinctiveness, inversion, and race on face recognition. In this paper we evaluate the ability of this theoretical framework to account for the effects of distinctiveness and race in four experiments in which white British and Japanese faces served as stimuli and both white British and Japanese students acted as subjects. In a recognition memory experiment the expected "own-race bias" was observed as a Race of Subject x Race of Face interaction. Distinctive faces were recognized more accurately than typical faces, but the effect of distinctiveness did not interact with the race of face or the race of subject. Typical faces were classified faster than distinctive faces in a task in which intact faces had to be distinguished from jumbled faces, as found in earlier work, and the effect of distinctiveness did not interact with the race of face or race of subject. In contrast, a task in which subjects classified faces according to their race did show a greater effect of distinctiveness for own-race faces. The results are discussed in relation to the two specific models within the multidimensional space framework identified by Valentine (1991a): a purely exemplar-based model and a norm-based coding model. It is argued that these results are more easily accommodated in terms of a purely exemplar-based model. Some conceptual problems in applying the norm-based coding model to the effect of race are discussed.

Adult↗
PubMed1993

Structural organization of the gene encoding the rat pancreatitis-associated protein. Analysis of its evolutionary history reveals an ancient divergence from the other carbohydrate-recognition domain-containing genes.

Rat pancreatitis-associated protein (PAP) mRNA is barely detectable in normal pancreas and overexpressed during acute pancreatitis (Iovanna, J., Orelle, B., Keim, V., and Dagorn J.-C. (1991) J. Biol. Chem. 266, 24664-24669). RNA amplification by reverse-transcriptase-coupled polymerase chain reaction showed that PAP mRNA was constitutively expressed in duodenum, jejunum, and ileum, at similar levels as in pancreas during the acute phase of pancreatitis. A weak expression was also detected in several other tissues. The rat PAP gene was isolated from a genomic library and characterized over 3.2 kilobases of gene sequence and 1.2 kilobases of 5'-flanking sequence. The 5' end of the coding sequence was determined by primer extension of the PAP transcript. Several potential regulatory elements were identified in the promoter region, including a pancreas-specific consensus sequence, two Pan1 (pancreas-specific) transcription activators, two IL-6 response elements, and one glucocorticoid response element. The PAP coding sequence spanned over six exons. The first three exons encoded the 5'-untranslated region of the mRNA, the signal peptide, and 39 amino acids of the NH2-terminal end of the mature protein, respectively. The other three exons encoded a domain of the protein with significant homology to the carbohydrate-recognition domain of animal lectins. Sequence comparison of the PAP gene with 13 carbohydrate-recognition domain-containing genes revealed that they derived from the same ancestor gene. Position of introns within the carbohydrate-recognition domain were different, however, suggesting that PAP belongs to a new group of lectins. These results support the hypothesis that genes encoding PAP and other lectins evolved from a common ancestor gene by intron gain.

Acute Disease↗