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 1,225 records · Page 68Linked to original sources
PubMed2001

Risk stratification for subclavian artery angioplasty: is there an increased rate of restenosis after stent implantation?

PURPOSE: To compare long-term patency after balloon angioplasty of stenotic or occluded subclavian arteries with and without adjunctive stenting and to identify independent risk factors for restenosis after balloon angioplasty. METHODS: In a retrospective cohort study, 115 consecutive patients (65 women; mean age 60 years, interquartile range 53-68) who underwent PTA for atherosclerotic subclavian artery obstruction within a 15-year period were included. Among these, 26 (23%) consecutive patients had Palmaz stents routinely implanted since 1996. Follow-up investigation was performed in the year 2000. Patency during the median 44-month follow-up period (interquartile range 18-69 months, minimum 12) was evaluated by oscillography, blood pressure measurement, and color-coded duplex sonography. The predictive value of possible risk factors for restenosis was assessed in a multivariate model controlling for cardiovascular comorbidities and angiographic data. RESULTS: PTA success was achieved in 98 (85%) patients, 72 (81%) of 89 undergoing angioplasty alone and all 26 with stents. Complete occlusion of the vessel and long lesions (> or = 2 cm) correlated with a lower success rate. One-year patency was 76% in unstented arteries and 95% in stented lesions due to better primary technical success, but at 4 years, the patency rates were 59% in arteries with stents and 68% in arteries without. Long lesions, residual stenosis after PTA, and stent implantation were independent predictors for restenosis after successful intervention. CONCLUSIONS: Subclavian arterial stent implantation is associated with better 1-year patency than PTA due to improved technical success, but intermediate and long-term outcomes are less favorable, as instent restenosis frequently occurs.

Aged↗
PubMed1990

Differential expression of Hox 3.1 protein in subregions of the embryonic and adult spinal cord.

Synthetic oligopeptides derived from the predicted Hox 3.1 protein coding sequence were used for the production of antibodies (anti-aa2) that specifically recognize Hox 3.1 protein in tissue sections. These antibodies were applied in immunohistochemical studies to monitor the expression of Hox 3.1 protein within the central nervous system (CNS) of embryonic and adult mice. We demonstrate congruency between the distinct Hox 3.1 RNA and protein expression patterns in the developing spinal cord by direct comparison of in situ hybridization and immunohistochemical staining in frozen sagittal sections from embryos of 12.5 days of gestation. A distinct pattern of spatially restricted expression of Hox 3.1 protein within the spinal cord was first detected at around 10.5 days of embryonic development. Within certain anteroposterior limits the geometries of this expression pattern change drastically during subsequent embryonic stages, concomitant with important cytoarchitectural changes in the developing spinal cord. Analyses on subcellular levels indicate predominant accumulation of Hox 3.1 protein within nuclei of neuronal cells. In addition to the nuclear localization in subsets of embryonic cells, persistent accumulation of Hox 3.1 protein was shown in nuclei of fully differentiated and mature neuronal cells of the adult CNS.

Animals↗
PubMed1987

The genome of herpes simplex virus: structure, replication and evolution.

The objectives of this paper are to discuss the structure and genetic content of the genome of herpes simplex virus type 1 (HSV-1), the nature of virus DNA replicative processes, and aspects of the evolution of the virus DNA, in particular those bearing on DNA replication. We are in the late stages of determining the complete sequence of the DNA of HSV-1, which contains about 155,000 base pairs, and thus the treatment is primarily from a viewpoint of DNA sequence and organization. The genome possesses around 75 genes, generally densely arranged and without long range ordering. Introns are present in only a few genes. Protein coding sequences have been predicted, and the functions of the proteins are being pursued by various means, including use of existing genetic and biochemical data, computer based analyses, expression of isolated genes and use of oligopeptide antisera. Many proteins are known to be virion structural components, or to have regulatory roles, or to function in synthesis of virus DNA. Many, however, still lack an assigned function. Two classes of genetic entities necessary for virus DNA replication have been characterized: cis-acting sequences, which include origins of replication and packaging signals, and genes encoding proteins involved in replication. Aside from enzymes of nucleotide metabolism, the latter include DNA polymerase, DNA binding proteins, and five species detected by genetic assays, but of presently unknown functions. Complete genome sequences are now known for the related alphaherpesvirus varicella-zoster virus and for the very distinct gammaherpesvirus Epstein-Barr virus. Comparisons between the three sequences show various homologies, and also several types of divergence and rearrangement, and so allow models to be proposed for possible events in the evolution of present day herpesvirus genomes. Another aspect of genome evolution is seen in the wide range of overall base compositions found in present day herpesvirus DNAs. Finally, certain herpesvirus genes are homologous to non-herpesvirus genes, giving a glimpse of more remote relationships.

Base Sequence↗
PubMed1988

Molecular cloning of bovine beta-lactoglobulin cDNA.

A cDNA library from bovine mammary gland mRNA was constructed in pBR322 and screened by hybrid-selected translation and immunoscreening. Several beta-lactoglobulin clones were identified and sequenced. All clones contained cDNA fragments corresponding to the 3' region of beta-lactoglobulin mRNA. The 3' non-translated region of beta-lactoglobulin mRNA consists of 187 nucleotides; the polyadenylation signal AATAAA occurs 17 nucleotides before the poly(A) tail. The amino-acid sequence predicted from the 3' coding region corresponds completely to the previously determined amino-acid sequence of beta-lactoglobulin.

Amino Acid Sequence↗
PubMed2006

Generating novel allelic variation through Activator insertional mutagenesis in maize.

The maize transposable element Activator (Ac) has been exploited as an insertional mutagen to disrupt, clone, and characterize genes in a number of plant species. To develop an Ac-based mutagenesis platform for maize, a large-scale mutagenesis was conducted targeting the pink scutellum1 locus. We selected 1092 Ac transposition events from a closely linked donor Ac, resulting in the recovery of 17 novel ps1 alleles. Multiple phenotypic classes were identified corresponding to Ac insertions in the 5'-UTR and coding region of the predicted Ps1 gene. To generate a stable allelic series, we employed genetic screens and identified 83 germinally heritable ps1 excision alleles. Molecular characterization of these excision alleles revealed a position-dependent bias in excision allele frequencies and the predominance of 7- and 8-bp footprint products. In total, 19 unique ps1 excision alleles were generated in this study, including several that resulted in weak mutant phenotypes. The analysis of footprint alleles suggests a model of Ac excision in maize that is consistent with recent in vitro studies of hAT element excision. Importantly, the genetic and molecular methods developed in this study can be extended to generate novel allelic variation at any Ac-tagged gene in the genome.

Alleles↗
PubMed2005

Human ERas gene has an upstream premature polyadenylation signal that results in a truncated, noncoding transcript.

The ERas gene is expressed in mouse embryonic stem (ES) cells and promotes their in vitro proliferation and tumorigenicity. We analyzed the expression of the human ERas gene in human ES cells by reverse transcription-polymerase chain reaction (RT-PCR) and serial analysis of gene expression but could not detect a full-length coding transcript. Sequence analysis predicted a premature polyadenylation signal for the human ERas transcript, which we confirmed by 3' RACE analysis. By RT-PCR, we identified a truncated noncoding transcript in human ES cells that is downregulated during differentiation, suggesting conserved tissue specificity of the promoter region. Previous reports and expressed sequence tag databases indicate that orthologues of this gene are expressed in other mammals, including the mouse, dog, and cow, which suggests that it became a silenced pseudogene relatively recently in mammalian evolution. In addition to the premature polyadenylation site, both the human and chimpanzee ERas genes include typical Alu-S retrotransposon insertions that could also influence expression at this locus. The lack of ERas expression in human ES cells suggests that they could have significantly different tumorigenic properties than mouse ES cells.

Animals↗
PubMed1998

A comprehensive evolutionary analysis based on nucleotide and amino acid sequences of the alpha- and beta-subunits of glycoprotein hormone gene family.

On the basis of nucleotide sequences of the coding region and their predicted amino acid sequences, 58 glycoprotein hormone subunit genes were compared, aligned and used to construct phylogenetic trees for this family. The analysis included 17 alpha-subunits, eight TSH beta-, six FSH beta-, 17 LH beta/CG beta-, four fish gonadotropin (GTH)-I beta-, five fish GTH-II beta- and one additional fish GTH beta-subunit. The reliability of the phylogenetic trees was probed with the bootstrapping test. Our results indicated that: both the alpha- and beta-subunits of the family diverged from a common ancestral gene about 927 million years ago, the initial precursor of the beta-subunit duplicated to give rise to the LH beta and a second hormone, the latter then duplicating to FSH beta and TSH beta, so that FSH beta is related more to TSH beta than to LH beta; and bony fish GTH-I beta is highly related to mammalian FSH beta, whereas the bony fish GTH-II beta is more related to mammalian LH beta. For scientific consistency and convenience, we propose that the following nomenclature be adopted, all fish gonadotropins of type I be classified as FSH and all type II be classified as LH hormones. In addition, on the basis of results from this and other studies, we propose an evolutionary history for this glycoprotein hormone family. Reconstruction of the evolutionary history of this family would not only provide clues to understanding thyrotropin and gonadotropin functions, but would also allow further revision of the present nomenclature of the gonadotropins in fish.

Amino Acid Sequence↗
PubMed2006

Identification and analysis of novel genes expressed in the mouse embryonic facial primordia.

Craniofacial anomalies are a common feature of human congenital dysmorphology syndromes, suggesting that genes expressed in the developing face are likely to play a wider role in embryonic development. To facilitate the identification of genes involved in embryogenesis, we previously constructed an enriched cDNA library by subtracting adult mouse liver cDNA from that of embryonic day (E)10.5 mouse pharyngeal arch cDNA. From this library, 273 unique clones were sequenced and known proteins binned into functional categories in order to assess enrichment of the library (1). We have now selected 31 novel and poorly characterised genes from this library and present bioinformatic analysis to predict proteins encoded by these genes, and to detect evolutionary conservation. Of these genes 61% (19/31) showed restricted expression in the developing embryo, and a subset of these was chosen for further in silico characterisation as well as experimental determination of subcellular localisation based on transient transfection of predicted full-length coding sequences into mammalian cell lines. Where a human orthologue of these genes was detected, chromosomal localisation was determined relative to known loci for human congenital disease.

Animals↗
PubMed2001

Homozygous deletion of CDKN2A (p16INK4a/p14ARF) but not within 1p36 or at other tumor suppressor loci in neuroblastoma.

Loss of heterozygosity of several specific genomic regions is frequently observed in neuroblastoma tumors and cell lines, but homozygous deletion (HD) is rare, and no neuroblastoma tumor suppressor gene (TSG) has yet been identified. We performed a systematic search for HD, indicative of a disrupted TSG, in a panel of 46 neuroblastoma cell lines. An initial search focused on a well-characterized consensus region of hemizygous deletion at 1p36.3, which occurs in 35% of primary neuroblastomas. Each cell line was screened with 162 1p36 markers, for a resolution of 13 kb within the consensus 1p36.3 deletion region and 350 kb throughout the remainder of 1p36. No HDs were detected. This approach was expanded to survey 21 known TSGs, specifically targeting intragenic regions frequently inactivated in other malignancies. HD was detected only at the CDKN2A (p16INK4a/p14ARF) gene at 9p21 and was observed in 4 of 46 cell lines. The observed region of HD included all exons of both CDKN2A and the closely linked CDKN2B (p15INK4b) gene for cell lines LA-N-6 and CHLA-174, all exons of CDKN2A but none of CDKN2B for CHLA-179, and only 104 bp within CDKN2A exon 2 for CHLA-101. All four deletions are predicted to inactivate the coding regions of both p16INK4a and p14ARF. HD was observed in corresponding primary tumor samples for CHLA-101 and CHLA-174 but was not present in constitutional samples. These results suggest that for neuroblastoma, large HDs do not occur within 1p36, most known TSGs are not homozygously deleted, and biallelic inactivation of CDKN2A may contribute to tumorigenicity in a subset of cases.

Blotting, Southern↗
PubMed2001

Monte Carlo simulation of charged particle transport in biomatter.

Knowledge of the microscopic distribution of interactions in irradiated matter is of fundamental importance for a mechanistic understanding of subsequent effects. This may be obtained by Monte Carlo codes which simulate event-by-event the transport of charged particles in matter. The development of such codes necessitates accurate interaction cross-sections for all the important collision processes. A semi-theoretical formalism has been developed and implemented in a Monte Carlo code which fairly accurately predicts energy-loss spectra for charged particle impact on water molecules. The extension of the formalism for establishing the necessary cross-sections for liquid/solid water (i.e. more realistic biomatter) is discussed and preliminary results are presented.

Carbon↗
PubMed2001

Leishmania mexicana: the circular DNA 1 (CD1) element contains genes encoding nucleotide-binding protein.

OBJECTIVE: To determine the nucleotide sequence of cloned CD1 fragments from Leishmania mexicana and find ORFs predicted to have protein coding function. METHODS: CD1 element was separated by CHEF and recovered by agarase, and the digested CD1 fragments were cloned into pZero vector. Nucleotide sequences were determined by the dideoxy chain termination method with the automatic sequencing system ALF using the M13 universal primers. Sequences were analyzed using GCG-PCGENE computer programs. RESULTS: The sequence with 4,385 nucleotides was determined and two ORFs were considered to have protein coding function (encoding nucleotide-binding protein). CONCLUSION: Genes encoding nucleotide-binding protein were identified from the amplified CD1 element of Leishmania mexicana.

Amino Acid Sequence↗
PubMed2003

A bioinformatics-based approach for the prediction and identification of novel proteins potentially involved in phosphorylation signalling pathways.

Together with the explosion in the availability of genome data of a number of organisms including human and mouse, various methods and programs for computational prediction of protein-coding genes and annotation of functional proteins have dramatically increased. For the last decade there has been intense interest in the role of protein phosphorylation which is involved in post-translation modification mechanisms critically regulating inter/intracellular communication, patho/physiological responses and homeostasis during many biological processes. In the present study a total of 202 functionally uncharacterized human full-coding cDNA sequences were investigated using a bioinformatics-based approach. Ten novel potential substrates for protein kinases have been identified which may play multiple roles in regulating intracellular phosphorylation signalling pathways. In addition, 5 of those may be involved in the human-only post-translation mechanism regulated by specific protein kinases. The data presented here therefore would greatly contribute toward the understanding of human molecular basis and cellular signalling networks.

Amino Acid Motifs↗
PubMed1992

[Preliminary use of recombinant glycoprotein 52kd as an antigen in the diagnosis of human cytomegalovirus infection].

Interest in the human cytomegalovirus (HCMV) mainly derives from its associations with congenital malformations, mental retardation, and severe or fatal infections in immunosuppressed individuals such as transplant patients, tumor and AIDS patients. It is evidenced that there has been a need for a rapid and sensitive methods to detect an ongoing acute infection. The recent studies showed that high titers of antibody to the glycoprotein 52kd are present in sera of patients undergoing acute HCMV infection. However, purification of individual glycoprotein from HCMV-infected cells is a daunting prospect. HCMV glycoprotein 52 kd expressed via recombinant DNA techniques are a promising approach to solve this problem. In order to evaluate the diagnostic value of the recombinant glycoprotein 52 kd antigenic code region for HCMV infection, we have used the polymerase chain reaction (PCR) and recombinant DNA techniques to construct successfully the high-level expression plasmid pHCMV containing the HCMV GP-52 kd antigenic code region, with the predicted protein at levels up to 20% in total bacterial protein. The expressed protein was purified from SDS-PAGE, used as an antigen in Western-blot, and reacted with 12 cases of the positive sera, 4 cases of the negative sera, following by reaction with HRP-labelled horse IgG antibody against human. The results indicated that the approach we are using to detect antibody to HCMV acute infection are as sensitive as general serological methods such as ELISA, with the advantages of easy preparation of antigen with high quantity, and clinical practicability.

Antibodies, Viral↗
PubMed2005

Novel mutations in GJA3 associated with autosomal dominant congenital cataract in the Indian population.

PURPOSE: Connexin 46 (Cx46) is crucial in the maintenance of lens homeostasis and it is known to be expressed mainly in the terminally differentiated lens fiber cells. The present study aimed to identify the spectrum of mutations in Connexin 46 in the Indian population. METHODS: PCR based Single Stranded Conformational Polymorphism (SSCP) analysis was used to screen sixty probands with nonsyndromic congenital cataract for mutations in the Cx46 gene (GJA3), followed by direct sequencing of samples that showed an electrophoretic shift. Mutation predicted to affect the coding sequence were subsequently analyzed in the entire pedigree. RESULTS: Two novel missense mutations were identified in Cx46. The mutation in Family 1 was characterized as R76G with a total cataract phenotype. A V28M missense mutation was identified in family 2, the cataract phenotype varied in its severity and the age of onset. The mutation was also identified in 2 unaffected individuals of the family and the intrafamilial variation of the disease suggests the possibility of a modifier gene(s) or the effects of environmental factors being involved. The mutation was identified in all the affected members in the family and found to be absent in 400 ethnically matched control chromosomes analyzed. CONCLUSIONS: We conclude that connexin 46 mutations might account for as much as 3.3% of the hereditary congenital cataract in the Indian population.

Adult↗
PubMed2006

[Artificial neural network in the prediction of nosocomial infection risk].

OBJECTIVE: To establish a model based on artificial neural network in the prediction of nosocomial infection risk. METHODS: Clinical data of 27,352 inpatients extracted from hospital information system were cleaned and coded, and the model of prediction in nosocomial infection risk was developed based on artificial neural network. RESULTS: The structure of artificial neural network is {16-6-1}-BP, and the fit rate of prediction was 0.9891. The area under ROC curve was 0.986. CONCLUSION: Artificial neural network model can be used as a tool for nosocomial infection forecasting, which can provide supplementary information for the diagnosis and control of nosocomial infection.

Cross Infection↗
PubMed1984

Legal issues and ethical dilemmas surrounding bone marrow transplantation in children.

Bone marrow transplantation is but one of numerous new medical technologies that have raised complex legal and ethical issues. Laws pertaining to medical advances have generally been passed in response to the need to resolve conflicts in judicial opinions rather than in anticipation of those issues which impinge on individual liberties. Bone marrow transplantation law is not an exception. It is, unfortunately, not a product of a planned dialogue between members of those disciplines that could contribute significantly to the development of model codes. Consequently it seems predictable that public policy concerning bone marrow transplantation may not be shaped by the leveling influence that the medical profession can bring to such discussions unless physicians take the initiative to lay the foundations for such dialogues. It is hoped that these discussions will help to enhance and not impede the application of bone marrow transplantation not only for more children but also for other conditions that are not currently treated successfully.

Bone Marrow Transplantation↗
PubMed1994

[Familial adenomatous polyposis].

Familial adenomatous polyposis is a rare genetic disease with a dominant mode of inheritance, involved in 1% of colorectal cancer. The APC gene, responsible for the disease, has been localized on the long arm of chromosome 5 and has recently been cloned and sequenced. Mutations predicted to alter the coding property of the APC gene have been reported in large series of adenomatous polyposis patients. Some of them have been correlated with an attenuated phenotype. A genetic test has been developed in affected families. Systematic screening of registered at-risk relatives has allowed a significant reduction of the median age at adenomatous polyposis diagnosis, and thus the incidence of colorectal cancer.

Adenomatous Polyposis Coli↗
PubMed1994

Identification of two V beta 7-specific viral superantigens.

The commonly used strains of laboratory mice have mouse mammary tumor viruses (MTV) integrated at various locations in their DNA. The number and position of these integrants varies from one strain of mouse to another. It has recently been shown that the genomes of many of the MTV code for superantigens. The predicted amino acid sequences of these superantigens and their specificity for TCR V beta differs for each MTV integrant. This study contains the predicted amino acid sequence and V beta specificity of two MTV superantigens that had not previously been analyzed. The results show that both of these MTV superantigens are specific for TCR that bear V beta 7, but unlike the MTV7 superantigen not for receptors bearing V beta 6 or V beta 8.1. The data also support the conclusion of previous studies that the COOH-terminal sequence of these proteins is a major factor in controlling their V beta reactivity.

Amino Acid Sequence↗