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PubMed2006

Event related potentials and the perception of intensity in facial expressions.

It is well known from everyday experience, that facial expressions of emotions can very much vary in intensity, e.g. ranging from mild anger to rage, or from uneasiness and mild fear to angst and panic. However, the effect of different intensities of facial expressions of emotion on event related potentials has yet not been studied. We therefore investigated 16 healthy participants with a gender decision task to male and female faces displaying angry, disgusted and fearful facial expressions varying in intensity (50%, 100%, 150%). Analysis of ERP data showed a significant increase in amplitude of the N170 by intensity, but not by type of emotion. The intensity induced negative variation was most pronounced between 200 and 600ms at electrodes P9 and P10. For this time segment, there was a clear linear relationship between intensity and degree of negative deflection. A dipole source localisation of the intensity effect using the difference waveform (150% minus 50% intensity) revealed two symmetrically positioned generators within the inferior temporo-occipital lobe. An emotion specific effect for disgust was further found at temporal electrode sites (FT7 and FT8) at around 350-400ms. Results are summarised in a two-phase model of emotion recognition, suggesting the existence of an initial monitoring process which codes saliency of incoming facial information. In a second step, the specific emotional content of faces is decoded in emotion specific recognition systems.

Adult↗

PubMed2000

Biological information transfer beyond the genetic code: the sugar code.

In the era of genetic engineering, cloning, and genome sequencing the focus of research on the genetic code has received an even further accentuation in the public eye. In attempting, however, to understand intra- and intercellular recognition processes comprehensively, the two biochemical dimensions established by nucleic acids and proteins are not sufficient to satisfactorily explain all molecular events in, for example, cell adhesion or routing. The consideration of further code systems is essential to bridge this gap. A third biochemical alphabet forming code words with an information storage capacity second to no other substance class in rather small units (words, sentences) is established by monosaccharides (letters). As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers, when the total of conceivable hexamers is calculated. In addition to the sequence complexity, the use of magnetic resonance spectroscopy and molecular modeling has been instrumental in discovering that even small glycans can often reside in not only one but several distinct low-energy conformations (keys). Intriguingly, conformers can display notably different capacities to fit snugly into the binding site of nonhomologous receptors (locks). This process, experimentally verified for two classes of lectins, is termed "differential conformer selection." It adds potential for shifts of the conformer equilibrium to modulate ligand properties dynamically and reversibly to the well-known changes in sequence (including anomeric positioning and linkage points) and in pattern of substitution, for example, by sulfation. In the intimate interplay with sugar receptors (lectins, enzymes, and antibodies) the message of coding units of the sugar code is deciphered. Their recognition will trigger postbinding signaling and the intended biological response. Knowledge about the driving forces for the molecular rendezvous, i.e., contributions of bidentate or cooperative hydrogen bonds, dispersion forces, stacking, and solvent rearrangement, will enable the design of high-affinity ligands or mimetics thereof. They embody clinical applications reaching from receptor localization in diagnostic pathology to cell type-selective targeting of drugs and inhibition of undesired cell adhesion in bacterial/viral infections, inflammation, or metastasis.

Animals↗

PubMedDate not supplied

Detection of protein coding sequences using a mixture model for local protein amino acid sequence.

Locating protein coding regions in genomic DNA is a critical step in accessing the information generated by large scale sequencing projects. Current methods for gene detection depend on statistical measures of content differences between coding and noncoding DNA in addition to the recognition of promoters, splice sites, and other regulatory sites. Here we explore the potential value of recurrent amino acid sequence patterns 3-19 amino acids in length as a content statistic for use in gene finding approaches. A finite mixture model incorporating these patterns can partially discriminate protein sequences which have no (detectable) known homologs from randomized versions of these sequences, and from short (< or = 50 amino acids) non-coding segments extracted from the S. cerevisiea genome. The mixture model derived scores for a collection of human exons were not correlated with the GENSCAN scores, suggesting that the addition of our protein pattern recognition module to current gene recognition programs may improve their performance.

Algorithms↗

PubMed1976

Storage and retrieval of SNOP-coded pathologic diagnoses using offsite computing and optical character recognizing systems.

A computerized cross-reference system for retrieving autopsy and surgical pathology cases on the basis of case number or diagnosis has been implemented. The system achieves economy and flexibility by using offsite computer service bureaus for job production, eliminating the need for expensive onsite equipment. Coded diagnoses may be typed using the OCR (Optical Character Recognition) font simultaneously with or separately from the clinical documentation. The flexibility of new OCR equipment permits production of machine-readable code sheets with an ordinary pencil and completely eliminates the need for typing. The system produces year-to-date books that list all diagnoses, on an accumulating basis, in alphabetic order by SNOP* topology, morphology, etiology and function, and will be compatible with SNOMed. Because all data are stored on magnetic tape, they may be manipulated and retrieved as desired through user programming. The initial setup cost was dollar 1,000 for programming and testing, and production runs and all report printing cost about dollar 1,000 per year (autopsies and surgical pathology cases), which is about 1.1 cents per diagnosis.

Computer Systems↗

PubMed1983

Activation of the genes for variant surface glycoproteins 117 and 118 in Trypanosoma brucei.

We have studied the activation of genes for VSGs (variant surface glycoproteins) in Trypanosoma brucei (strain 427) in six independently isolated trypanosome clones; four expressing the gene for VSG 118 and two the gene for VSG 117. In all cases, gene activation is brought about by a duplicative transposition of the gene to an expression site located close to the end of a chromosome. The DNA segments flanking the expression-linked extra gene copy are nearly devoid of restriction enzyme recognition sites and their lengths vary by more than 10,000 base-pairs among different variants. From the correspondence of five upstream restriction sites, we conclude that the same expression site is used in each case. The transposition event does not lead to detectable alterations in the sequence coding for the mature protein. All restriction enzyme recognition sites detected in the basic copy gene are present also in each of the expression-linked copies. This argues against the introduction of mutations by an error-prone polymerase during the synthesis of the expression-linked copy. In five of the six variants, the 3' end of the VSG messenger RNA differs from that of the corresponding basic copy gene by multiple point mutations, insertions and deletions, starting at positions varying from 16 nucleotides upstream to 113 downstream of the last codon of the mature protein. We attribute this end alteration to the recombination process that introduces the gene into the expression site. We confirm that the expression-linked gene copy is more sensitive to DNase I than the corresponding basic copy gene. This appears to be due to its activated state and not to its location near the end of a chromosome, because another basic copy VSG gene permanently located near a chromosome end is not hypersensitive to DNase I. The mature transcripts of the 117 and 118 genes all possess the same 35 nucleotides at their 5' ends and these are not encoded contiguously in the basic gene copies with the remainder of the mRNAs. This extends our previous conclusion, that mature VSG mRNAs are formed by a splicing process in which the 35-nucleotide sequence encoded in the expression site is fused onto the body of the mRNA contributed by the transposed gene.

Animals↗

PubMed1999

Identification and cloning of rat galectin-2: expression is predominantly in epithelial cells of the stomach.

A complementary DNA clone preferentially expressed in the gastrointestinal tract was obtained from a rat stomach library. The protein coded by the clone had a single carbohydrate recognition domain having conserved motifs for beta-galactoside binding and showed 67% amino acid identity with human galectin-2. The recombinant protein synthesized in Escherichia coli could bind to an asialofetuin column and was eluted with beta-galactopyranoside. From these observations, we named the protein rat galectin-2 coded by the cDNA. The rat galectin-2 was predominantly expressed in the epithelial cells of stomach. Thus this protein may form a mucin layer cross-linking with the beta-galactoside moiety of glycoproteins.

Amino Acid Sequence↗

PubMed1985

Tactual perception of embossed Morse code and braille: the alliance of vision and touch.

In three experiments observers made visual matches to tangible embossed patterns. Stained glass was used to blur vision and thus allow the effect of visual guidance of tactual exploration on the accuracy of symbol recognition to be evaluated. Stained glass rendered the embossed code invisible, but allowed sight of the hand. In the first experiment subjects identified patterns made up of dots and dashes drawn from Morse code; in the second and third experiments they studied braille. The results show that subjects are more accurate in 'reading' tangible codes when provided with visual guidance. Performance was higher for braille than for Morse code. Vision aided touch through the provision of a frame of reference and through sight of scanning movements. Naive sighted observers were able to identify invisible braille dots by watching other individuals touch the symbols, suggesting the importance of vision of kinesthetic patterns.

Female↗

PubMed2005

Tobacco industry opposition to designating environmental tobacco smoke through E-codes.

This manuscript examines the public policy importance of 1993, United States Department of Health and Human Services actions to require doctors and hospitals to report a new external cause of injury code or E-code for environmental tobacco smoke related to causes of death such as lung cancer and severe heart disease. Methods included a qualitative archival analysis of all previously internal tobacco industry documents, pertinent newspaper and magazine articles, Americans for Nonsmokers' Rights database, and pertinent websites regarding environmental tobacco smoke and E-codes from 1993 to 1998. The E-code has continued to the present because of scientific and administrative recognition that environmental tobacco smoke is conclusively linked to illness and death. The industry argued that the E-code was unnecessary because of costs to business and no conclusive scientific evidence linking environmental tobacco smoke with pulmonary and cardiovascular deaths. This regulatory action based on current scientific evidence and medical decision-making contradicts the industry's claim that no deaths are conclusively associated with environmental tobacco smoke.

Cardiovascular Diseases↗

PubMed1992

Comparison of speech recognition ability with different speech processing strategies by Korean cochlear implantees.

Many variables affect the audiologic performance of cochlear implantees. With current methods of evaluation, it is difficult to directly compare auditory function with different speech coding strategies. We compared the audiologic performance directly with F0F1F2 and multipeak speech coding strategies in the same implanted ear of eight Korean cochlear implantees. We tested word and phoneme recognition abilities using Korean word lists for speech audiometry and two-syllable nonsense words, respectively. With the multipeak coding strategy, a significant difference in discrimination ability was found in the initial fricative consonant phonemes (/s/,/ss/,/h/). Our results suggest that the improvement of speech recognition ability with the multipeak coding strategy comes primarily from the better understanding of the initial fricative consonants.

Adult↗

PubMed1987

In vitro sodium bisulfite mutagenesis of restriction endonuclease recognition sites.

Sodium bisulfite treatment of single-stranded DNA deaminates exposed cytosine residues to form uracil, resulting in cytosine-to-thymidine transition mutations following DNA replication. We have used this reaction in vitro to destroy the recognition sequences for the restriction endonucleases HindIII and XmaI in the aminoglycoside 3'-phosphotransferase I coding region of plasmid pUC4K. This procedure should be applicable to the mutation of any recognition sequence of restriction endonucleases which generate cytosine-containing single-stranded ends. The possibility of mutagenesis of restriction sites to generate stop codons in coding regions is discussed.

Base Sequence↗

PubMed2002

A novel fold recognition method using composite predicted secondary structures.

In this work, we introduce a new method for fold recognition using composite secondary structures assembled from different secondary structure prediction servers for a given target sequence. An automatic, complete, and robust way of finding all possible combinations of predicted secondary structure segments (SSS) for the target sequence and clustering them into a few flexible clusters, each containing patterns with the same number of SSS, is developed. This program then takes two steps in choosing plausible homologues: (i) a SSS-based alignment excludes impossible templates whose SSS patterns are very different from any of those of the target; (ii) a residue-based alignment selects good structural templates based on sequence similarity and secondary structure similarity between the target and only those templates left in the first stage. The secondary structure of each residue in the target is selected from one of the predictions to find the best match with the template. Truncation is applied to a target where different predictions vary. In most cases, a target is also divided into N-terminal and C-terminal fragments, each of which is used as a separate subsequence. Our program was tested on the fold recognition targets from CASP3 with known PDB codes and some available targets from CASP4. The results are compared with a structural homologue list for each target produced by the CE program (Shindyalov and Bourne, Protein Eng 1998;11:739-747). The program successfully locates homologues with high Z-score and low root-mean-score deviation within the top 30-50 predictions in the overwhelming majority of cases.

Algorithms↗

PubMed1995

High-level secretion of hirudin by Hansenula polymorpha--authentic processing of three different preprohirudins.

A DNA sequence coding for a subtype of the hirudin variant HV1 was expressed in the methylotrophic yeast Hansenula polymorpha from a strongly inducible promoter element derived from a gene of the methanol metabolism pathway. For secretion, the coding sequence was fused to the KEX2 recognition site of three different prepro segments engineered from the MF alpha 1 gene of Saccharomyces cerevisiae, the glucoamylase (GAM1) gene of Schwanniomyces occidentalis and the gene for a crustacean hyperglycemic hormone from the shore crab Carcinus maenas. In all three cases, correct processing of the precursor molecule and efficient secretion of the mature protein were observed. In fermentations on a 10-1 scale of a transformant strain harbouring a MF alpha 1/hirudin-gene fusion yields in the range of grams per litre could be obtained. The majority of the secreted product was identified as the full-length 65-amino-acid hirudin. Only small amounts of a truncated 63-amino- acid product, frequently observed in S. cerevisiae-based expression systems, could be detected.

Amino Acid Sequence↗

PubMed1992

Reading isolated words: no evidence for automatic incorporation of the phonetic code.

Backward masking with a homophonic mask induces better target recognition than backward masking with a graphemic mask that shares the same letters with the target as the homophonic mask. From this, the existence of automatic prelexical phonological recoding in silent word reading has been inferred. The present experiments, however, show that the advantage of homophonic masks in a backward-masking task only arises if a considerable proportion of the masks are phonologically related to the targets (at least for Dutch). The results are in line with findings of lexical-decision tasks and number-processing tasks, and constitute a further argument for the dominance of the orthographic route over the phonological route in processing isolated written words.

Adult↗

PubMed1986

RAM, a gene of yeast required for a functional modification of RAS proteins and for production of mating pheromone a-factor.

We have identified a gene (SUPH) of S. cerevisiae that is required for both RAS function and mating by cells of a mating type. supH is allelic to ste16, a gene required for the production of the mating pheromone a-factor. Both RAS and a-factor coding sequences terminate with the potential acyltransferase recognition sequence Cys-A-A-X, where A is an aliphatic amino acid. Mutations in SUPH-STE16 prevent the membrane localization and maturation of RAS protein, as well as the fatty acid acylation of it and other membrane proteins. We propose the designation RAM (RAS protein and a-factor maturation function) for SUPH and STE16. RAM may encode an enzyme responsible for the modification and membrane localization of proteins with this C-terminal sequence.

Acylation↗

PubMed1995

Genomic organization and chromosomal localization of the human and mouse genes encoding the alpha receptor component for ciliary neurotrophic factor.

Ciliary neurotrophic factor (CNTF) has recently been found to share receptor components with, and to be structurally related to, a family of broadly acting cytokines, including interleukin-6, leukemia inhibitory factor, and oncostatin M. However, the CNTF receptor complex also includes a CNTF-specific component known as CNTF receptor alpha (CNTFR alpha). Here we describe the molecular cloning of the human and mouse genes encoding CNTFR. We report that the human and mouse genes have an identical intron-exon structure that correlates well with the domain structure of CNTFR alpha. That is, the signal peptide and the immunoglobulin-like domain are each encoded by single exons, the cytokine receptor-like domain is distributed among 4 exons, and the C-terminal glycosyl phosphatidylinositol recognition domain is encoded by the final coding exon. The position of the introns within the cytokine receptor-like domain corresponds to those found in other members of the cytokine receptor superfamily. Confirming a recent study using radiation hybrids, we have also mapped the human CNTFR gene to chromosome band 9p13 and the mouse gene to a syntenic region of chromosome 4.

Amino Acid Sequence↗

PubMed2005

The role of phonological activation in the visual semantic retrieval of Chinese characters.

The Stroop paradigm was used to examine the role of phonological activation in semantic access and its development in reading Chinese characters. Subjects (age 7-23 years) of different reading ability were asked to name the display color of Chinese characters. The characters were displayed in four different colors: red, yellow, blue and green. There were five types of relationships between a character and its display color: semantically congruent, phonologically congruent, semantically incongruent, phonologically incongruent and neutral. In addition to the classical Stroop effects, interference and facilitation effects from the homophones of color characters were also observed. The younger children and those with lower reading ability exhibited stronger Stroop effects. These findings suggest that phonological codes are activated automatically in Chinese character recognition. Furthermore, there is more phonological activation in the semantic retrieval of children in lower grades and those with lower reading ability.

Adult↗

PubMed2004

Differences in facial expressions of four universal emotions.

The facial action coding system (FACS) was used to examine recognition rates in 105 healthy young men and women who viewed 128 facial expressions of posed and evoked happy, sad, angry and fearful emotions in color photographs balanced for gender and ethnicity of poser. Categorical analyses determined the specificity of individual action units for each emotion. Relationships between recognition rates for different emotions and action units were evaluated using a logistic regression model. Each emotion could be identified by a group of action units, characteristic to the emotion and distinct from other emotions. Characteristic happy expressions comprised raised inner eyebrows, tightened lower eyelid, raised cheeks, upper lip raised and lip corners turned upward. Recognition of happy faces was associated with cheek raise, lid tightening and outer brow raise. Characteristic sad expressions comprised furrowed eyebrow, opened mouth with upper lip being raised, lip corners stretched and turned down, and chin pulled up. Only brow lower and chin raise were associated with sad recognition. Characteristic anger expressions comprised lowered eyebrows, eyes wide open with tightened lower lid, lips exposing teeth and stretched lip corners. Recognition of angry faces was associated with lowered eyebrows, upper lid raise and lower lip depression. Characteristic fear expressions comprised eyes wide open, furrowed and raised eyebrows and stretched mouth. Recognition of fearful faces was most highly associated with upper lip raise and nostril dilation, although both occurred infrequently, and with inner brow raise and widened eyes. Comparisons are made with previous studies that used different facial stimuli.

Adolescent↗

PubMedDate not supplied

Contribution of NF-kappaB and p53 in the glutamate-induced apoptosis.

Exposure of primary cultures of cerebellar granule cells for 15 min to micromolar concentrations of glutamate results in cell death of both necrotic and apoptotic types. Among the intracellular events triggered by glutamate, we identified two transcriptional factors: the p50 member of the NF-kappaB family and the tumor suppressor phosphoprotein p53. Pretreatment of the cultures with aspirin, which inhibits NF-kappaB activation, or with specific p53 antisense oligonucleotide, which inhibits p53 transcription, resulted in a complete prevention of glutamate-induced p53 induction and apoptosis. These findings suggest the existence of a transcriptional program activated by glutamate receptor stimulation in which p50 and p53 play a relevant role. Then, we studied the expression of two p53 downstream genes that could participate in the glutamate-induced pro-apoptotic pathway: p21, which codes for an inhibitor of different cyclin dependent kinases, and MSH2, which codes for a protein involved in the recognition and repair of DNA mismatches. We found that primary cerebellar neurons expressed p21 and MSH2 at very low levels in basal conditions. However, very soon after a brief exposure of the cells to glutamate, the expression of both proteins was dramatically enhanced.On these bases, we propose NF-kappaB, p53, p21 and MSH2 as relevant contributors of the glutamate-induced pro-apoptotic pathway. Understanding this cascade of nuclear events may unravel specific targets for pharmacological intervention for those neurological diseases in which excitatory amino acid-induced apoptosis plays a relevant role.

Aging↗