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PubMedDate not supplied

Representing nursing assessments in clinical information systems using the logical observation identifiers, names, and codes database.

In recent years, the Logical Observation Identifiers, Names, and Codes (LOINC) Database has been expanded to include assessment items of relevance to nursing and in 2002 met the criteria for "recognition" by the American Nurses Association. Assessment measures in LOINC include those related to vital signs, obstetric measurements, clinical assessment scales, assessments from standardized nursing terminologies, and research instruments. In order for LOINC to be of greater use in implementing information systems that support nursing practice, additional content is needed. Moreover, those implementing systems for nursing practice must be aware of the manner in which LOINC codes for assessments can be appropriately linked with other aspects of the nursing process such as diagnoses and interventions. Such linkages are necessary to document nursing contributions to healthcare outcomes within the context of a multidisciplinary care environment and to facilitate building of nursing knowledge from clinical practice. The purposes of this paper are to provide an overview of the LOINC database, to describe examples of assessments of relevance to nursing contained in LOINC, and to illustrate linkages of LOINC assessments with other nursing concepts.

Computational Biology↗

PubMed1981

Heart disease program for school children and high school students in Osaka City: an introduction of computer assisted ECG analysis system as a screening tool.

Fukuda ECP-100 computer assisted ECG analysis system was introduced into the heart disease program for school children and high school students in Osaka City in 1979. This analysis system was used as screening tool and 39,532 of 4th graders of primary schools were examined during the first year. To evaluate and improve this analysis system a "pilot study" was organized and 52 school physicians and 10 specialists made up a "working group". "Urgent reference codes" were set to be printed out so that the limitation of the present system of the Heart Disease Program should be compensated. Problems of the ECG analysis system were as follows. The Q wave registered too wide and there were same difficulties in recognizing the end point of the T wave. Recognition ot tiny "r" wave seemed to be impossible and base line sway seemed responsible for numerous erroneous outputs. Some cases corresponding to code "4-n-n" were found to be normal after further examination. This system can be said to be useful as a screening tool. Using this system at least 4 cases of serious lesion were newly detected, one case of myocarditis and 3 cases of myocardial diseases.

Adolescent↗

PubMed1978

Involvement of H-2L gene products in virus-immune T-cell recognition. Evidence for an H-2L-restricted T-cell response.

The H-2L locus is closely linked to H-2D and codes for antigenic specificities present on a 45,000 mol wt glycoprotein that is distinct from the molecule which bears the D region private specificity. It was found that BALB/c-H-2db mice, which lack detectable cell-surface H-2L gene products, were able to generate influenza- and vaccinia-immune cytotoxic T cells which lyse D region-compatible target cells, although they have been reported to be incapable of making a similar response to ectromelia virus (7). Thus, the lack of H-2L antigenic specificities does not produce a general loss of responsiveness for other viruses even when a highly cross-reactive pox virus (vaccinia) was studied. Antisera-blocking experiments utilizing sera specific for either L or D molecules indicated that BALB/c mice generate influenza virus-immune cytotoxic T-cell subsets which independently recognize H-2L and H-2D gene products in association with viral antigens. These results are the first indication that products of the H-2L locus can operate analogously to H-2K/D gene products in virus-immune T-cell recognition.

Animals↗

PubMed1993

Molecular analysis of a t(11;14)(q23;q11) from a patient with null-cell acute lymphoblastic leukemia.

/lp;&-3qChromosome 11, band q23, is the frequent site of recurring cytogenetic rearrangements in human leukemia. We have cloned and sequenced the breakpoint junctions from a patient who had null-cell acute lymphoblastic leukemia (ALL) with a t(11;14)(q23;q11). The chromosome 14 breakpoints occurred within the TCRD locus, close to two diversity segments. The chromosome 11 breakpoint occurred between two head-to-head heptamer sequences, and junctional diversity was evident at both derivative junctions, suggesting involvement of the V(D)J recombinase. The TCRA/D locus on the normal chromosome 14 had undergone a V delta 2-D delta 3-psi J alpha joining. Two phage clones with this VDJ rearrangement were isolated; one of these contained an intra-J alpha region deletion. Two clones with the derivative 11 junction were isolated; one of these had a similar, but not identical, deletion. A heptamer-nonamer recognition sequence (located approximately 70 kb 5' to C alpha), not associated with a TCR gene coding segment, was found in the immediate vicinity of both 5' breakpoints. We have designated this sequence 5'del for 5' deleting element. An intra-J alpha region deletion involving this heptamer-nonamer was previously identified in the leukemia cells recovered from a patient who had T-cell ALL. Fifty kilobases of DNA on 11q23 surrounding the breakpoint were cloned and analyzed. No CpG islands or conserved sequences were identified within this region.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1999

The stationary statistical properties of human coding sequences.

We introduce a generally applicable method for the discovery and quantitation of all of the characteristic statistical properties of a class of biological sequences, given examples from the class. This method employs a reversible binary encoding of sequences into the binary digits -1 and +1. Then, provided that the sample is sufficient, the sample cumulants on the subsets of digit positions will manifest all of the statistical properties of the class. As an illustration, we present the main results of a complete characterization of the stationary statistical properties of human coding sequences, in terms of their sample cumulants. Many of the telling sample cumulants are described.

Base Sequence↗

PubMed2000

The olfactory receptor gene superfamily: data mining, classification, and nomenclature.

The vertebrate olfactory receptor (OR) subgenome harbors the largest known gene family, which has been expanded by the need to provide recognition capacity for millions of potential odorants. We implemented an automated procedure to identify all OR coding regions from published sequences. This led us to the identification of 831 OR coding regions (including pseudogenes) from 24 vertebrate species. The resulting dataset was subjected to neighbor-joining phylogenetic analysis and classified into 32 distinct families, 14 of which include only genes from tetrapodan species (Class II ORs). We also report here the first identification of OR sequences from a marsupial (koala) and a monotreme (platypus). Analysis of these OR sequences suggests that the ancestral mammal had a small OR repertoire, which expanded independently in all three mammalian subclasses. Classification of "fish-like" (Class I) ORs indicates that some of these ancient ORs were maintained and even expanded in mammals. A nomenclature system for the OR gene superfamily is proposed, based on a divergence evolutionary model. The nomenclature consists of the root symbol 'OR', followed by a family numeral, subfamily letter(s), and a numeral representing the individual gene within the subfamily. For example, OR3A1 is an OR gene of family 3, subfamily A, and OR7E12P is an OR pseudogene of family 7, subfamily E. The symbol is to be preceded by a species indicator. We have assigned the proposed nomenclature symbols for all 330 human OR genes in the database. A WWW tool for automated name assignment is provided.

Animals↗

PubMed1983

Sequence relationships between Kirsten retrovirus genomes and the genomes of other murine retroviruses.

RNA sequence relationships between the genomes of the Kirsten murine sarcoma virus (MSV-K) complex, the Kirsten murine leukemia virus (MuLV-K) complex, the Gross murine leukemia virus (MuLV-G), and the Moloney murine leukemia virus (MuLV-M) were investigated. Sedimentation analyses revealed the expected 30 and 34 S RNA subunits in the MSV-K complex and a previously undetected 30 S RNA subunit accompanying the 34 S RNA subunit in the MuLV-K complex. Nucleic acid hybridization data indicated that each Kirsten virus 30 S RNA subunit had about 40% sequence homology with the RNA genome of MuLV-G, although these sequences were only partially homologous between the two 30 S subunits. In contrast, the MuLV-K 34 S RNA subunit had 96% sequence homology with the MuLV-G genome, whereas the MSV-K 34 S RNA subunit displayed only 71% sequence homology with the MuLV-G genome. Similar relationships were indicated by oligonucleotide fingerprinting. The oligonucleotide data, taken with published sequence data on the MuLV-G and MuLV-M genomes, enabled us to construct partial sequence maps of the MuLV-K 34 S RNA subunit and the MSV-K 34 and 30 S RNA subunits. The sequence arrangements indicated that (1) the MuLV-K 34 S RNA subunit is a variant of the MuLV-G genome; (2) the MSV-K 34 S RNA subunit is a recombinant molecule, which maintains the length of its leukemia virus parent; and (3) the MSV-K 30 S RNA subunit may have been generated from the MuLV-K 34 S genome by a two-stage process, culminating in the retention of parental sequences only within the U5 and U3 noncoding segments and within several amino-terminal coding segments. Further examination of published retrovirus genome sequences revealed several strategically situated sets of potential recognition signals for transcription and translation and suggested a model for genetic recombination based on mRNA splicing signals and areas of limited sequence homology. This model may explain how foreign gene elements can be inserted into retrovirus genomes to generate either functional or defective recombinant retroviruses.

AKR murine leukemia virus↗

PubMed1992

The 7SL RNA homologue of Trypanosoma brucei is closely related to mammalian 7SL RNA.

In eukaryotes, protein translocation across the endoplasmic reticulum is mediated by a signal recognition particle, a small ribonucleoprotein (RNP) containing 7SL RNA. We have cloned and sequenced the gene coding for the Trypanosoma brucei 7SL RNA homologue and found that its sequence shows the highest degree of similarity to the human 7SL RNA sequence. In keeping with the prototype secondary structure of eukaryotic 7SL RNA, the trypanosome 7SL RNA secondary structure can be folded into four domains. The 7SL RNP, which sediments at approximately 11S on sucrose density gradients, was partially purified using column chromatography. A particle containing a 76-nucleotide-long RNA co-purified with the 7SL RNP; however, these particles did not co-fractionate by non-denaturing polyacrylamide gel electrophoresis.

Animals↗

PubMed1991

Expression of a biologically active ovine trophoblastic interferon using a baculovirus expression system.

Ovine trophoblast protein (oTP) an embryonic interferon, which plays a key role in maternal recognition of pregnancy, has been expressed in insect cells using a baculovirus expression system. A cDNA coding for oTP was inserted downstream of the strong polyhedrin promoter. Cells infected with recombinant virus produced biologically active oTP and greater than 90% was secreted into the culture medium during infection. High amount of antiviral activity were produced (up to 5 x 10(5) IU per ml of culture medium). Recombinant oTP (roTP) was purified by immunoaffinity chromatography and found to be identical to authentic oTP with respect to molecular mass and N-terminal amino acid sequence.

Amino Acid Sequence↗

PubMed2000

A recurrent model of transformation invariance by association.

This paper describes an investigation of a recurrent artificial neural network which uses association to build transform-invariant representations. The simulation implements the analytic model of Parga and Rolls [(1998). Transform-invariant recognition by association in a recurrent network. Neural Computation 10(6), 1507-1525.] which defines multiple (e.g. "view") patterns to be within the basin of attraction of a shared (e.g. "object") representation. First, it was shown that the network could store and correctly retrieve an "object" representation from any one of the views which define that object, with capacity as predicted analytically. Second, new results extended the analysis by showing that correct object retrieval could occur where retrieval cues were distorted; where there was some association between the views of different objects; and where connectivity was diluted, even when this dilution was asymmetric. The simulations also extended the analysis by showing that the system could work well with sparse patterns; and showing how pattern sparseness interacts with the number of views of each object (as a result of the statistical properties of the pattern coding) to give predictable object retrieval performance. The results thus usefully extend a recurrent model of invariant pattern recognition.

Artificial Intelligence↗

PubMed1987

Primary structure of human placental anticoagulant protein.

The primary structure of human placental anticoagulant protein was determined by a combination of amino acid and nucleotide sequencing techniques. The carboxymethylated protein was digested with cyanogen bromide, and the resulting peptides were separated by gel filtration and high-performance liquid chromatography. A total of 239 out of 319 amino acid residues were identified from 7 cyanogen bromide fragments. A full-length cDNA clone encoding placental anticoagulant protein was isolated from a human placenta cDNA library. This clone was 1.6 kilobases long and contained a translation initiation site coding for methionine, 957 nucleotides encoding for the mature protein, a stop codon, a poly(A) recognition site, and a poly(A) tail. Analysis of the tryptic-blocked peptide that originated from the NH2-terminus of the protein showed that the terminal methionine was removed and the adjacent alanine residue was acetylated by posttranslational events. Placental anticoagulant protein is composed of 319 amino acids with acetylalanine as the NH2-terminus and has a high degree of sequence identity with lipocortins I and II. It contains four internal repeats, each including a sequence corresponding to a putative Ca2+-dependent phospholipid binding site. Placental anticoagulant protein is a member of the lipocortin/calpactin family.

Amino Acid Sequence↗

PubMedDate not supplied

Variable expression of Ia antigens on the vascular endothelium of mouse skin allografts.

Ia antigens are membrane-bound glycoproteins that play a part in antigen recognition and subsequent cell-cell interactions in the immune response. In the mouse they are coded for by the I region of the major histocompatibility complex H-2 and have been demonstrated on B lymphocytes, monocytes, activated T cells, macrophages and dendritic cells, including Langerhans cells. Ia-like antigens have also been detected on the vascular endothelium in man and on epidermal keratinocytes in rats but expression on the latter cells was induced by a graft-versus-host reaction or by contact hypersensitivity. In the mouse, previous studies have suggested that Ia antigens in skin are restricted to epidermal Langerhans cells and it was thought that these were the targets for Ia-dependent rejection of skin allografts. The results presented here show that Ia antigens in mouse allografts are also present on the vascular endothelium but their expression is variable and dependent on the immunological status of the recipient. These findings suggest that vascular endothelial cells can act as targets in Ia-incompatible skin allograft rejection.

Animals↗

PubMed2001

Mutation screening of the muscarinic M(2) and M(3) receptor genes in normal and asthmatic subjects.

1. Muscarinic receptors are important in the development of airway hyperresponsiveness, and dysfunction of these receptors has been suggested to be present in asthma. 2. The human muscarinic M(2) and M(3) receptor genes were screened for polymorphic variation using single-stranded conformation polymorphism (SSCP) analysis, complemented by direct fluorescent sequencing. Forty-six random DNA samples and 46 respiratory physician diagnosed asthmatic samples were used as a template for analysis. 3. Within the muscarinic M(2) receptor gene, we identified two degenerate single base substitutions (1197T-->C, Thr-->Thr and 976A-->C, Arg-->Arg) in one random and one asthmatic sample respectively. Analysis of the 3' UTR region revealed an additional 'A' at bp 1793 (c.f. ATG). This was present in all of 49 samples analysed by sequencing or BsmI digest, suggesting that the published sequence (GenBank Accession NO: M16404) is incorrect. A common 3' UTR polymorphism (T-->A) was found at bp 1696 (c.f. ATG) (allelic frequency=65%, n=60), but this does not alter transcription factor recognition sites. 4. We were unable to identify any polymorphic variation within the muscarinic M(3) coding region or the flanking regions investigated, using the methods described. 5. The coding regions for the human muscarinic M(2) and M(3) receptor genes are both highly conserved. These data suggest that polymorphic variation within these coding sequences is unlikely to account for inter-individual variability in response to methacholine or anticholinergic therapy. The potential functional significance of the muscarinic M(2) receptor 3' UTR polymorphism (bp 1696) remains to be determined.

3' Untranslated Regions↗

PubMed2006

Oligonucleotides suppress IL-8 in skin keratinocytes in vitro and offer anti-inflammatory properties in vivo.

DNA codes for genetic information. Furthermore, recent findings suggest that DNA offers additional function, particularly in the recognition of microorganisms. In this study, we investigated two classes of oligodeoxynucleotides (ODN) in skin keratinocytes; namely, an ODN comprising two cytidine-phosphate-guanosine (CpG) motifs (CpG-1-phosphorothioate (PTO)) and a poly-cytidine (Non-CpG-5-PTO) as control. Both fluorescence-tagged ODN were rapidly taken up by cells and accumulated already after 5 minutes in perinuclear compartments. In order to test whether ODN convey immunological effects in keratinocytes, secretion of IL-8 was measured. Interestingly, both CpG-1-PTO and Non-CpG-5-PTO suppressed basal and tumor necrosis factor alpha-induced IL-8 levels measured in cell culture supernatants. Experiments using deletion mutant revealed a critical length of approximately 16 nucleotides conveying IL-8 suppression. Studies regarding the ODN backbone offered that PTO bondings are critical for significant IL-8 suppression. In order to substantiate the anti-inflammatory response, a contact hypersensitivity mouse model was utilized. Topical application of Non-CpG-5-PTO-containing ointments reduced ear thickness in sensitized mice. Taken together, these findings suggest an anti-inflammatory effect of ODN in epithelial cells in vitro and in vivo, indicating that DNA molecules offer distinct biological activities restricted to the physiological compartment applied. This effect seems to be independent from Toll-like receptor 9.

Administration, Topical↗

PubMed1997

Glycoprotein changes in tumours: a renaissance in clinical applications.

1. Oligosaccharides linked to protein (glycoprotein) or lipid (glycolipid) are the major components at the outer surface of mammalian cells. Studies using antibodies and lectins have shown in the past that the oligosaccharides they recognize exhibit tumour-associated changes, i.e. they are carbohydrate tumour-associated antigens. 2. The oligosaccharides have been further characterized in recent years by structural analysis using high-resolution chromatographic techniques, MS and NMR. NMR gives an oligosaccharide finger-print that is characteristic of monosaccharide type and linkage and which can be correlated with magnetic resonance spectroscopic data on fine-needle tissue aspirates. 3. Also of relevance is the new understanding of the molecular biology of MUC genes, which code for mucin protein backbones, and of the glycosyltransferase genes, which determine oligosaccharide structure and immunological recognition. 4. For these reasons, we believe that tumour-associated oligosaccharide changes should be revisited in the context of what we now know about structure and expression. This review synopsizes the past data using the detection of carbohydrate tumour-associated antigens by binding of lectins and antibodies, and puts it into the context of NMR fingerprints or signatures.

Antigens, Tumor-Associated, Carbohydrate↗

PubMed1997

Functional analysis of the mouse myelin/oligodendrocyte glycoprotein gene promoter in the oligodendroglial CG4 cell line.

Myelin/oligodendrocyte glycoprotein (MOG) is a late phylogenetic acquisition among vertebrates that is found only in mammals. MOG is a minor component of myelin protein, representing approximately 0.01-0.05% of the total. Regulatory elements in the MOG gene were identified by transfecting the oligodendroglial CG4 cell line with chimeric MOG-luciferase genes. Only a few hundred base pairs upstream of the coding sequence were necessary for high-level activity of the mouse MOG promoter. More distal recognition sites may exist, because silencing activity, indicative of negative regulatory elements, was detected upstream of base pair 657. Transcriptional activity of chimeric MOG- and myelin basic protein-luciferase genes was greater in CG4 cells than in 3T3 fibroblasts or C6 glioblastoma, demonstrating their superiority for functional analysis of myelin gene regulatory elements.

Animals↗

PubMed1988

Tactile recognition of mirror images by children: intermanual transfer and rotation of the palm.

In order to evaluate the importance of the axis of stimulus presentation, inter- and intramanual recognition of mirror pairs was studied with the stimulus materials aligned along the front/back axis (whereas in previous work the mirror pairs were aligned along the left/right axis). Children were allowed to feel shapes with the whole hand, with only four fingers (excluding the thumb), or with only the index finger. After learning with one hand, recognition was tested in experiment 1 with the other hand; after learning with one orientation of the hand (palm down or up), recognition was tested in experiment 2 with the other orientation (palm up or down) of the same hand; after learning with one coronal alignment of the hand (to the left or right), recognition was tested in experiment 3 with the other alignment (to the right or left), but without rotation, of the same hand. Significantly fewer intermanual recognition errors were made on mirror pairs with the materials oriented along the front/back axis than in previous work when oriented along the left/right axis. This supports the suggestion that such errors arise when the stimuli are oriented along the left/right axis during formation of the memory trace. The same trend was unexpectedly obtained for intramanual recognition errors (after rotation of the hand). These errors (after hand rotation) are largely due to coding with respect to the hand; they are reduced when the hand is not aligned with the body axis, since then coding can also occur in relation to the environment.

Attention↗

PubMed2006

From the Academy: Colloquium review. Unique characteristics of Xanthomonas oryzae pv. oryzae AvrXa21 and implications for plant innate immunity.

This article provides a brief overview of some of the major concepts and molecular features of plant and animal innate immune systems. The rice pathogen recognition receptor, XA21, confers resistance to Xanthomonas oryzae pv. oryzae strains producing the AvrXa21 elicitor. Xa21 codes for a receptor-like kinase consisting of an extracellular leucine-rich repeat domain, a transmembrane domain, and a cytoplasmic kinase domain. We show that AvrXa21 activity requires the presence of rax (required for AvrXa21) A, raxB, and raxC genes that encode components of a type one secretion system. In contrast, an hrpC(-) strain deficient in type three secretion maintains AvrXa21 activity. Xanthomonas campestris pv. campestris can express AvrXa21 activity if raxST, encoding a putative sulfotransferase, and raxA are provided in trans. Expression of rax genes depends on population density and other functioning rax genes. This and other data suggest that the AvrXa21 pathogen-associated molecule is involved in quorum sensing. Together these data suggest that AvrXa21 represents a previously uncharacterized class of Gram-negative bacterial signaling molecules. These results from our studies of the XA21/AvrXa21 interaction call for some modifications in the way we think about innate immunity strategies.

Animals↗