Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Predictive coding”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,369 records · Page 76Linked to original sources
PubMed1988

The structure and organization of the human heavy neurofilament subunit (NF-H) and the gene encoding it.

Genomic clones for the largest human neurofilament protein (NF-H) were isolated, the intron/exon boundaries mapped and the entire protein-coding regions (exons) sequenced. The predicted protein contains a central region that obeys the structural criteria identified for alpha-helical 'rod' domains typically present in all IF protein components: it is approximately 310 amino acids long, shares amino acid sequence homology with other IF protein rod domains and displays the characteristic heptad repeats of apolar amino acids which facilitate coiled-coil interaction. Nevertheless, anomalies are noted in the structure of the NF-H rod which could explain observations of its poor homopolymeric assembly in vitro. The protein segment on the carboxy-terminal side of the human NF-H rod is uniquely long (greater than 600 amino acids) compared to other IF proteins and is highly charged (greater than 24% Glu, greater than 25% Lys), rich in proline (greater than 12%) and impoverished in cysteine, methionine and aromatic amino acids. Its most remarkable feature is a repetitive sequence that covers more than half its length and includes the sequence motif, Lys-Ser-Pro (KSP) greater than 40 times. Together with the recent identification of the serine in KSP as the main target for NF-directed protein kinases in vivo, this repetitive character explains the massive phosphorylation of the NF-H subunit that can occur in axons. The human NF-H gene has three introns, two of which interrupt the protein-coding sequence at identical points to introns in the genes for the two smaller NF proteins, NF-M and NF-L.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1990

Perceived pitch of vibrotactile stimuli: effects of vibration amplitude, and implications for vibration frequency coding.

1. The effect of changes in amplitude on the perceived pitch of cutaneous vibratory stimuli was studied in psychophysical experiments designed to test whether the coding of information about the frequency of the vibration might be based on the ratio of recruitment of the PC (Pacinian corpuscle-associated) and RA (rapidly adapting) classes of tactile sensory fibres. The study was based on previous data which show that at certain vibration frequencies (e.g. 150 Hz) the ratio of recruitment of the PC and RA classes should vary as a function of vibration amplitude. 2. Sinusoidal vibration at either 30 Hz or 150 Hz, and at an amplitude 10 dB above subjective detection thresholds was delivered in a 1 s train to the distal phalangeal pad of the index finger in eight human subjects. This standard vibration was followed after 0.5 s by a 1 s comparison train of vibration which (unknown to the subject) was at the same frequency as the standard but at a range of amplitudes from 2 to 50 dB above the detection threshold. A two-alternative forced-choice procedure was used in which the subject had to indicate whether the comparison stimulus was higher or lower in pitch (frequency) than the standard. 3. Marked differences were seen from subject to subject in the effect of amplitude on perceived pitch at both 30 Hz and 150 Hz. At 150 Hz, five out of the eight subjects reported an increase in pitch as the amplitude of the comparison vibration increased, one experienced no change, and only two experienced the fall in perceived pitch that is predicted if the proposed ratio code contributes to vibrotactile pitch judgements. At 30 Hz similar intersubject variability was seen in the pitch-amplitude functions. 4. The results do not support the hypothesis that a ratio code contributes to vibrotactile pitch perception. We conclude that temporal patterning of impulse activity remains the major candidate code for pitch perception, at least over a substantial part of the vibrotactile frequency bandwidth.

Female↗
PubMed1992

Structure prediction and modelling.

Cracking the second fundamental code of molecular biology (how the tertiary structure of a protein is determined by its amino acid sequence) remains an elusive goal. However, the impetus to establish credible approximations, if not a definitive solution to this relationship, has never been greater. In the past year significant progress has been made through a series of novel approaches. This review describes the most important developments and outlines how they can be usefully employed by those whose specialization lies outside the field.

Models, Molecular↗
PubMed1994

Affect, verbal content, and psychophysiology in the arguments of couples with a violent husband.

The purpose of this investigation was to study the affect, psychophysiology, and violent content of arguments in couples with a violent husband. On the basis of self-reports of violent arguments, there were no wife behaviors that successfully suppressed husband violence once it began; moreover, husband violence escalated in response to nonviolent as well as violent wife behaviors, whereas wife violence escalated only in reaction to husband violence or emotional abuse. Only wives were fearful during violent and nonviolent arguments. The observational coding of nonviolent arguments in the laboratory revealed that both battering husbands and their wives (DV) were angrier than their maritally distressed but nonviolent (DNV) counterparts. As predicted, on the more provocative anger codes, only DV men differed from their DNV counterparts. However, DV wives were as verbally aggressive toward their husbands as DV husbands were toward their wives.

Adult↗
PubMed2005

Prediction of protein secondary structure using improved two-level neural network architecture.

In this paper we propose constructing an improved two-level neural network to predict protein secondary structure. Firstly, we code the whole protein composition information as the inputs to the first-level network besides the evolutionary information. Secondly, we calculate the reliability score for each residue position based on the output of the first-level network, and the role of the second-level network is to take full advantage of the residues with a higher reliability score to impact the neighboring residues with a lower one for improving the whole prediction accuracy. Thirdly, considering it is indeed a problem that the target protein can be lost in the multiple sequence alignment we propose to code single sequence into the second-level network. The experimental results show that our proposed method can efficiently improve the prediction accuracy.

Algorithms↗
PubMed1991

Characterization of a full-length cDNA which codes for the human spermidine/spermine N1-acetyltransferase.

Spermidine/spermine N1-acetyltransferase is the rate-limiting enzyme in the catabolism of cellular polyamines. Using a combination of cDNA library screening and anchored PCR methodologies, a full length cDNA designated AP3/F7 corresponding to the human SSAT was cloned using RNA from the human large cell undifferentiated lung carcinoma line NCI H157. The resulting cDNA clone is 1,060 base pairs with a 513 base open reading frame coding for a 171 amino acid protein, with a predicted subunit molecular weight of 20,023. The 5' non-coding region of AP3/F7 is 165 bases and the 3' untranslated region is 382 bases with a polyadenylation site 20 bases 5' to the poly(A) tail. This full length cDNA should be an aid in the study of the regulation of spermidine/spermine N1-acetyltransferase expression and the significance of the acetyltransferase in polyamine metabolism.

Acetyltransferases↗
PubMed2004

Exploring tick saliva: from biochemistry to 'sialomes' and functional genomics.

Tick saliva, a fluid once believed to be only relevant for lubrication of mouthparts and water balance, is now well known to be a cocktail of potent anti-haemostatic, anti-inflammatory and immunomodulatory molecules that helps these arthropods obtain a blood meal from their vertebrate hosts. The repertoire of pharmacologically active components in this cocktail is impressive as well as the number of targets they specifically affect. These salivary components change the physiology of the host at the bite site and, consequently, some pathogens transmitted by ticks take advantage of this change and become more infective. Tick salivary proteins have therefore become an attractive target to control tick-borne diseases. Recent advances in molecular biology, protein chemistry and computational biology are accelerating the isolation, sequencing and analysis of a large number of transcripts and proteins from the saliva of different ticks. Many of these newly isolated genes code for proteins with homologies to known proteins allowing identification or prediction of their function. However, most of these genes code for proteins with unknown functions therefore opening the road to functional genomic approaches to identify their biological activities and roles in blood feeding and hence, vaccine development to control tick-borne diseases.

Animals↗
PubMed1985

Structure and expression of amplified cKi-ras gene sequences in Y1 mouse adrenal tumor cells.

A recombinant library of double minute chromosomal DNA, enriched in specific sequences that are amplified in Y1 mouse adrenal tumor cells, was used as a source of material to explore the structure and expression of amplified cKi-ras genes in these cells. From DNA sequence analysis of these cloned fragments, we found no evidence for the presence of point mutations previously demonstrated to be associated with activation of the transforming potential of ras genes. A comparison of the mouse gene with that of the homologous human cKi-ras2 gene reveals 94% nucleotide sequence homology within the coding regions and 97% homology for the predicted amino acid composition. Like the human gene, the mouse cKi-ras gene contains alternative 3' coding exons. Blot hybridization analyses of RNA revealed a preferential utilization of the more 3' of the two fourth coding exons in the generation of Y1 cKi-ras transcripts.

Adrenal Gland Neoplasms↗
PubMed2006

Unspecified falls among youth: predictors of coding specificity in the emergency department.

BACKGROUND: Deficiencies in emergency department (ED) charting is a common international problem. While unintentional falls account for the largest proportion of injury related ED visits by youth, insufficient charting details result in more than one third of these falls being coded as "unspecified". Non-specific coding compromises the utility of injury surveillance data. OBJECTIVE: To re-examine the ED charts of unspecified youth falls to determine the possibility of assigning more specific codes. METHODS: 400 ED charts for youth (aged 0-19 years) treated at four EDs in an urban Canadian health region between 1997 and 1999 and coded as "Other or unspecified fall" (ICD-9 E888) were randomly selected. A structured chart review was completed and a blinded nosologist recoded the cause of injury using the extracted data. Differences in coding specificity were compared with the original data, and logistic regression was undertaken to examine variables that predicted assignment of a specific E-code. RESULTS: A more specific code was assigned to 46% of cases initially coded as unspecified. Of these, 73% were recoded as "Slips, trips, and stumbles" (E885), which still lacks the specificity required for injury prevention planning; 2% of charts had no fall documented. Multivariate analysis revealed that dichotomized injury severity (adjusted odds ratio (OR) = 1.75 (95% confidence interval, 1.11 to 2.78)), arrival at the ED by ambulance (adjusted OR = 5.41 (1.07 to 27.0)), and the availability of nurse's notes or triage forms, or both, in the chart (adjusted OR = 3.75 (2.17 to 6.45)) were the strongest predictors of a more specific E-code assignment. CONCLUSIONS: Deficiencies in both chart documentation and coding specificity contribute to the use of non-specific E-codes. More comprehensive triage coding, improved chart documentation, and alternative methods of data collection in the acute care setting are required to improve ED injury surveillance initiatives.

Accidental Falls↗
PubMed2004

Trends in the sensitivity, positive predictive value, false-positive rate, and comparability ratio of hospital discharge diagnosis codes for acute myocardial infarction in four US communities, 1987-2000.

Variations in the validity of hospital discharge diagnoses can complicate the assessment of trends in incidence of acute myocardial infarction (AMI). To clarify trends in the validity of discharge codes, the authors compared event classification based on published Atherosclerosis Risk in Communities (ARIC) Study criteria with the presence or absence of an International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) hospital discharge code for AMI (code 410). Between 1987 and 2000, 154,836 coronary heart disease events involving hospitalization in the four ARIC communities had ICD-9-CM codes screened for AMI. The sensitivity of ICD-9-CM code 410 for classifying AMI in men (sensitivity = 0.65, 95% confidence interval (CI): 0.63, 0.66) was statistically significantly greater than that found for women (sensitivity = 0.60, 95% CI: 0.58, 0.62) and was greater in Whites (sensitivity = 0.67, 95% CI: 0.65, 0.68) than in Blacks (sensitivity = 0.50, 95% CI: 0.47, 0.53). The ethnic difference was related to a greater frequency of hypertensive heart disease and congestive heart failure codes encompassing AMI among Blacks as compared with Whites. The authors found that although the validity of ICD-9-CM code 410 to identify AMI was generally stable from 1987 through 2000, differences between Blacks and Whites and across geographic locations support investment in validation efforts in ongoing surveillance studies.

Adult↗
PubMed1991

[Code of codon roots of amino acids and idiotypic networks].

Novel models of idiotype nets of antibodies have been developed to study the code responsible for the amino acid interaction and complex formation of proteins. It is shown that the interaction of protein active centres in idiotype nets can be interpreted and predicted basing on the structure of code of codon roots of amino acids and polarity principle. "Internal images" of the sequence antigen determinants of proteins in immunoglobulin molecules are built mainly from the amino acid groups having common codon roots, which is in agreement with the conception of the structure of the root code.

Amino Acid Sequence↗
PubMed2004

A comparative method for finding and folding RNA secondary structures within protein-coding regions.

Existing computational methods for RNA secondary-structure prediction tacitly assume RNA to only encode functional RNA structures. However, experimental studies have revealed that some RNA sequences, e.g. compact viral genomes, can simultaneously encode functional RNA structures as well as proteins, and evidence is accumulating that this phenomenon may also be found in Eukaryotes. We here present the first comparative method, called RNA-DECODER, which explicitly takes the known protein-coding context of an RNA-sequence alignment into account in order to predict evolutionarily conserved secondary-structure elements, which may span both coding and non-coding regions. RNA-DECODER employs a stochastic context-free grammar together with a set of carefully devised phylogenetic substitution-models, which can disentangle and evaluate the different kinds of overlapping evolutionary constraints which arise. We show that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD.

Codon↗
PubMed2006

Validity of International Classification of Diseases, Ninth Revision, Clinical Modification Codes for Acute Renal Failure.

Administrative and claims databases may be useful for the study of acute renal failure (ARF) and ARF that requires dialysis (ARF-D), but the validity of the corresponding diagnosis and procedure codes is unknown. The performance characteristics of International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes for ARF were assessed against serum creatinine-based definitions of ARF in 97,705 adult discharges from three Boston hospitals in 2004. For ARF-D, ICD-9-CM codes were compared with review of medical records in 150 patients with ARF-D and 150 control patients. As compared with a diagnostic standard of a 100% change in serum creatinine, ICD-9-CM codes for ARF had a sensitivity of 35.4%, specificity of 97.7%, positive predictive value of 47.9%, and negative predictive value of 96.1%. As compared with review of medical records, ICD-9-CM codes for ARF-D had positive predictive value of 94.0% and negative predictive value of 90.0%. It is concluded that administrative databases may be a powerful tool for the study of ARF, although the low sensitivity of ARF codes is an important caveat. The excellent performance characteristics of ICD-9-CM codes for ARF-D suggest that administrative data sets may be particularly well suited for research endeavors that involve patients with ARF-D.

Acute Kidney Injury↗
PubMed2004

A novel elastin gene mutation resulting in an autosomal dominant form of cutis laxa.

BACKGROUND: Cutis laxa is an extremely rare disorder characterized by marked skin laxity. Few cases of cutis laxa have been described worldwide. Clinical presentation and mode of inheritance show considerable heterogeneity; autosomal dominant, autosomal recessive, and X-linked recessive forms have been reported. Only 3 mutations in the elastin gene have been described as the genetic cause of the autosomal dominant form of cutis laxa. OBSERVATIONS: A 45-year-old woman and her 19-year-old son presented with inelastic, loose-hanging, and wrinkled skin that appeared prematurely aged and were clinically diagnosed as having cutis laxa. Mutational analysis of the elastin gene evidenced a novel mutation (2292delC) that predicts a frameshift in the coding region and causes translation to proceed into the 3'-untranslated region. This would replace the C-terminal amino acid of the normal elastin protein with a novel sequence. CONCLUSION: This article is the fourth report of autosomal dominant cutis laxa to appear in the literature in which a mutation in the elastin gene has been correlated with the disease.

Adult↗
PubMed2005

Role of beta-galactosidase and elastin binding protein in lysosomal and nonlysosomal complexes of patients with GM1-gangliosidosis.

G(M1)-gangliosidosis is a lysosomal storage disorder caused by a deficiency of beta-galactosidase (GLB1). The GLB1 gene gives rise to the GLB1 lysosomal enzyme and to the elastin binding protein (EBP), involved in elastic fiber deposition. GLB1 forms a complex with protective protein cathepsin A (PPCA), alpha neuraminidase (NEU1), and galactosamine 6-sulphate sulfatase (GALNS) inside lysosomes, while EBP binds to PPCA and NEU1 on the cell surface. We investigated the function of the GLB1 and EBP mutated proteins by analyzing the clinical, genetic, and cellular data of 11 G(M1)-gangliosidosis patients. Their molecular analysis, followed by expression studies, lead to the identification of four new and 10 known GLB1 mutations. Some common amino acid substitutions [c.1445G>A (p.Arg482H), c.622C>T (p.Arg208His), c.175C>T (p.Arg59Cys) and c.176G>A (p.Arg59His)] were present in the GLB1 enzyme of several patients, all of Mediterranean origin, suggesting a common origin. Western blotting analyses against GLB1, EBP, and PPCA proteins showed that the identified mutations affect GLB1 enzyme activity and/or stability. The c.1445G>A (p.Arg482His), c.175C>T (p.Arg59Cys), c.733+2T>C, c.1736G>A (p.Gly579Asp), and c.1051C>T (p.Arg351X) GLB1 mutations, affect the stabilization of PPCA probably because they hamper the interaction between GLB1/EBP and PPCA within the multiprotein complex. The amount of EBP was normal, but the detection of impaired elastogenesis in such patients suggests an alteration in its function. We conclude that the presence of genetic lesions in both GLB1 and EBP coding region does not directly predict impaired elastogenesis and that elastic fiber assembly has to be evaluated specifically in each case. Nevertheless, the degree of EBP involvement may be linked to specific clinical findings.

Adult↗
PubMed2001

Human biotin-containing subunit of 3-methylcrotonyl-CoA carboxylase gene (MCCA): cDNA sequence, genomic organization, localization to chromosomal band 3q27, and expression.

3-Methylcrotonyl-CoA carboxylase (MCCase; EC 6.4.1.4) is a mitochondrial biotin enzyme and plays an essential role in the catabolism of leucine and isovalerate in animals, bacterial species, and plants. MCCase consists of two subunits, those that are biotin-containing and non-biotin-containing. The genes responsible for these subunits have been isolated in soybean, Arabidopsis thaliana, and tomatoes, but not in mammals. In humans, MCCase deficiency has been thought to be a rare metabolic disease, but the number of patients with MCCase deficiency appears to be increasing with a wide range of clinical presentations, some that result in a lethal condition and others that are asymptomatic. In this report, we have isolated and carried out chromosomal mapping of the gene for the biotin-containing subunit (A subunit) of the human MCCase gene, MCCA. The cDNA predicts an open reading frame coding for a 725-amino-acid protein with mitochondrial signal peptide, biotin carboxylase, and biotin-carrier domains. The gene is composed of at least 19 exons and covers more than 70 kb of sequence on band q27 of chromosome 3. MCCA was abundantly expressed in mitochondria-rich organs, such as the heart, skeletal muscles, kidney, and liver. In exon 13, we observed a His/Pro polymorphism at codon 464 (an A to C transition at nucleotide position 1391 in the cDNA sequence). Then, we determined the DNA sequences of the 5' untranslated region and entire coding regions in two patients with MCCase deficiency, but no sequence substitution was detected, suggesting that the gene mutations might be in the non-biotin-containing subunit (B subunit) gene, MCCB, in these patients.

Amino Acid Sequence↗
PubMed1995

Molecular cloning of the cDNA encoding a stress-inducible protein phosphatase 1 (PP1) catalytic subunit from French bean (Phaseolus vulgaris L.).

A cDNA showing high sequence similarity (> 70%) to plant protein phosphatase 1 catalytic subunit variants from other species has been isolated from a cDNA library derived from mRNAs expressed in elicitor-treated suspension-cultured cells. The clone appears to be a near full-length 1431 bp with a 172 bp 5'-untranslated region and a 317 bp 3'-untranslated region. The open reading frame, determined by sequence similarity, codes for a protein with predicted M(r) of 35,552. Alternatively an ATG situated to the 5' end of the putative start site would increase the protein size by 6 amino acids. The mRNA for Pvpp1 was shown to be rapidly induced by elicitor treatment of suspension-cultured cells of French bean. The cloned cDNA represents one of the few examples of a gene product that is probably involved in dephosphorylation events arising after the initial responses to biotic stress.

Amino Acid Sequence↗
PubMed1994

Molecular cloning and characterization of the Schizosaccharomyces pombe his3 gene for use as a selectable marker.

A DNA fragment which carries the his3 gene of Schizosaccharomyces pombe has been isolated and characterized for use as a selectable marker in transformations. The his3 gene encodes the imidazole acetol phosphate transaminase enzyme (E.C.2.6.1.9), which is responsible for converting imidazole acetol-P to histidinol-P in step 8 of histidine biosynthesis. The nucleotide sequences of a 2196 bp gene fragment and a corresponding cDNA clone were determined. Three intron sequences punctuate the 1451 bp coding region which generates a predicted polypeptide of 384 amino acids with a molecular mass of 42736 daltons. Northern analysis of his3 mRNAs indicates that the transcript is approximately 1.6 kb in size. Steady-state levels are down-regulated by nitrogen limitation but are unaffected by histidine starvation. The deduced amino acid sequence was compared to the Saccharomyces cerevisiae HIS5, Escherichia coli HisC, and Salmonella typhimurium HisC proteins, all of which are imidazole acetol phosphate transaminases. The S. pombe his3 protein was 49.5% identical to the S. cerevisiae HIS5 protein and 21.5% identity was found when all four proteins were compared. The shuttle vector pBG1 was constructed by subcloning the smallest functional region of his3 and the S. pombe ars1 sequence into pUC18 for use in transformation of His3--S. pombe strains. New S. pombe strains in which the his3 gene was deleted have also been constructed.

Amino Acid Sequence↗