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PubMed1993

Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids.

We present a method to determine the location and extent of protein binding regions in nucleic acids by computer-assisted analysis of sequence data. The program ConsIndex establishes a library of consensus descriptions based on sequence sets containing known regulatory elements. These defined consensus descriptions are used by the program ConsInspector to predict binding sites in new sequences. We show the programs to correctly determine the significant regions involved in transcriptional control of seven sequence elements. The internal profile of relative variability of individual nucleotide positions within these regions paralleled experimental profiles of biological significance. Consensus descriptions are determined by employing an anchored alignment scheme, the results of which are then evaluated by a novel method which is superior to cluster algorithms. The alignment procedure is able to include several closely related sequences without biasing the consensus description. Moreover, the algorithm detects additional elements on the basis of a moderate distance correlation and is capable of discriminating between real binding sites and false positive matches. The software is well suited to cope with the frequent phenomenon of optional elements present in a subset of functionally similar sequences, while taking maximal advantage of the existing sequence data base. Since it requires only a minimum of seven sequences for a single element, it is applicable to a wide range of binding sites.

Algorithms↗
PubMed2000

Severity of coronary artery calcification by electron beam computed tomography predicts silent myocardial ischemia.

BACKGROUND: Detection of subclinical coronary artery disease (CAD) before the development of life-threatening cardiac complications has great potential clinical relevance. Electron beam computed tomography (EBCT) is currently the only noninvasive test that can detect CAD in all stages of its development and thus has the potential to be an excellent screening technique for identifying asymptomatic subjects with underlying myocardial ischemia. METHODS AND RESULTS: Over 2.5 years, we prospectively studied 3895 generally asymptomatic subjects with EBCT, 411 of whom had stress myocardial perfusion tomography (SPECT) within a close (median, 17 days) time period. SPECT and exercise treadmill results were compared with the coronary artery calcium score (CACS) as assessed by EBCT. The total CACS identified a population at high risk for having myocardial ischemia by SPECT although only a minority of subjects (22%) with an abnormal EBCT had an abnormal SPECT. No subject with CACS <10 had an abnormal SPECT compared with 2.6% of those with scores from 11 to 100, 11.3% of those with scores from 101 to 399, and 46% of those with scores >/=400 (P<0.0001). CACS predicted an abnormal SPECT regardless of subject age or sex. CONCLUSIONS: CACS identifies a high-risk group of asymptomatic subjects who have clinically important silent myocardial ischemia. Our results support the role of EBCT as the initial screening tool for identifying individuals at various stages of CAD development for whom therapeutic decision making may differ considerably.

Adult↗
PubMed1990

Melting and chemical modification of a cyclized self-splicing group I intron: similarity of structures in 1 M Na+, in 10 mM Mg2+, and in the presence of substrate.

C IVS is the cyclized form of the intron from the RNA precursor of the Tetrahymena thermophila large subunit (LSU) ribosomal RNA. C IVS was mapped by chemical modification in 1 M Na+, 0.05 M Na+ and 10 mM Mg2+ (Na+/Mg2+), and Na+/Mg2+ with CUCU substrate. The results suggest the secondary structure is similar for all three conditions. Optical melting curves were also measured for C IVS in 1 M Na+ and Na+/Mg2+ and indicate the secondary structures have similar stabilities under both conditions. Computer predictions of secondary structure and stability are in good agreement with observations. The results suggest that many of the approximations used for computer prediction of secondary structure by free energy minimization are reasonable.

Aldehydes↗
PubMed2005

Bone tissue engineering using polycaprolactone scaffolds fabricated via selective laser sintering.

Polycaprolactone (PCL) is a bioresorbable polymer with potential applications for bone and cartilage repair. In this work, porous PCL scaffolds were computationally designed and then fabricated via selective laser sintering (SLS), a rapid prototyping technique. The microstructure and mechanical properties of the fabricated scaffolds were assessed and compared to the designed porous architectures and computationally predicted properties. Scaffolds were then seeded with bone morphogenetic protein-7 (BMP-7) transduced fibroblasts and implanted subcutaneously to evaluate biological properties and to demonstrate tissue in-growth. The work done illustrates the ability to design and fabricate PCL scaffolds with porous architecture that have sufficient mechanical properties for bone tissue engineering applications using SLS. Compressive modulus and yield strength values ranged from 52 to 67 MPa and 2.0 to 3.2 Mpa, respectively, lying within the lower range of properties reported for human trabecular bone. Finite element analysis (FEA) results showed that mechanical properties of scaffold designs and of fabricated scaffolds can be computationally predicted. Histological evaluation and micro-computed tomography (microCT) analysis of implanted scaffolds showed that bone can be generated in vivo. Finally, to demonstrate the clinical application of this technology, we designed and fabricated a prototype mandibular condyle scaffold based on an actual pig condyle. The integration of scaffold computational design and free-form fabrication techniques presented here could prove highly useful for the construction of scaffolds that have anatomy specific exterior architecture derived from patient CT or MRI data and an interior porous architecture derived from computational design optimization.

Animals↗
PubMed2006

MHCPred 2.0: an updated quantitative T-cell epitope prediction server.

UNLABELLED: The accurate computational prediction of T-cell epitopes can greatly reduce the experimental overhead implicit in candidate epitope identification within genomic sequences. In this article we present MHCPred 2.0, an enhanced version of our online, quantitative T-cell epitope prediction server. The previous version of MHCPred included mostly alleles from the human leukocyte antigen A (HLA-A) locus. In MHCPred 2.0, mouse models are added and computational constraints removed. Currently the server includes 11 human HLA class I, three human HLA class II, and three mouse class I models. Additionally, a binding model for the human transporter associated with antigen processing (TAP) is incorporated into the new MHCPred. A tool for the design of heteroclitic peptides is also included within the server. To refine the veracity of binding affinities prediction, a confidence percentage is also now calculated for each peptide predicted. AVAILABILITY: As previously, MHCPred 2.0 is freely available at the URL http://www.jenner.ac.uk/MHCPred/ CONTACT: Darren R. Flower (darren.flower@jenner.ac.uk).

Algorithms↗
PubMed2004

DNA sequence alterations affect nucleosome array formation of the chicken ovalbumin gene.

The role of the large amount (more than half of the genome) of noncoding DNA in higher organisms is not well understood. DNA evolved to function in the context of chromatin, and the possibility exists that some of the noncoding DNA serves to influence chromatin structure and function. In this age of genomics and bioinformatics, genomic DNA sequences are being searched for informational content beyond the known genetic code. The discovery that period-10 non-T, A/T, G (VWG) triplets are among the most abundant motifs in human genomic DNA suggests that they may serve some function in higher organisms. In this paper, we provide direct evidence that the regular oscillation of period-10 VWG that occurs in the chicken ovalbumin gene sequence with a dinucleosome-like period facilitates nucleosome array formation. Using a linker histone-dependent in vitro chromatin assembly system that spontaneously aligns nucleosomes into a physiological array, we show that nucleosomes tend to avoid DNA regions with low period-10 VWG counts. This avoidance leads to the formation of an array with a nucleosome repeat equal to half the period value of the oscillation in period-10 VWG, as determined by Fourier analysis. Two different half-period deletions in the wild-type DNA sequence altered the nucleosome array, as predicted computationally. In contrast, a full-period deletion had an insignificant effect on the nucleosome array formed, also consistent with the prediction. An inversion mutation, with no DNA sequences deleted, again altered the nucleosome array formed, as predicted computationally. Hence, a VWG dinucleosome signal is plausible.

Animals↗
PubMedDate not supplied

F18-fluorodeoxyglucose single-photon emission computed tomography predicts functional outcome of dyssynergic myocardium after surgical revascularization.

BACKGROUND: Prediction of functional recovery after revascularization is possible with positron emission tomography and F18-fluorodeoxyglucose (FDG). Recently, the use of FDG in combination with single-photon emission computed tomography (SPECT), with 511 keV collimators, has been proposed to allow more widespread use of FDG. In the current study we aimed to predict improvement of regional left ventricular function after surgical revascularization with FDG and SPECT. METHODS AND RESULTS: Twenty-seven patients with regional wall motion abnormalities (on echocardiography) underwent early thallium-201 (Tl-201) SPECT to assess perfusion and FDG SPECT to assess regional glucose uptake. The left ventricular myocardium was divided into 13 segments. For each segment, tracer uptake was evaluated visually (with the use of a 4-point scoring system) by consensus of two observers. Myocardial viability was determined in dyssynergic segments on echocardiography and defined as normal perfusion or increased FDG uptake in a perfusion defect (mismatch). Absence of viability was defined as a perfusion defect without increased FDG uptake (match). Improvement of regional wall motion was assessed 3 months after revascularization. In the group of segments that were viable on FDG/Tl-201 SPECT (n = 64), the segmental wall motion score decreased from 1.4 +/- 0.5 to 0.6 +/- 0.7 (p < 0.01), whereas the segmental wall motion score remained unchanged in nonviable segments (n = 72): 1.6 +/- 0.5 versus 1.5 +/- 0.6 (not significant). Forty-six (72%) of the 64 segments that were viable on FDG/Tl-201 SPECT demonstrated improved contractile function after coronary revascularization. In contrast, only 7 (10%) of 72 nonviable segments on FDG/Tl-201 SPECT showed improvement in function after revascularization (p < 0.01 versus viable segments). The sensitivity, specificity, and positive and negative predictive values were 87%, 78%, 72%, and 90%, respectively. CONCLUSION: This study shows that FDG/Tl-201 SPECT can identify patients who improve in regional ventricular function after revascularization.

Aged↗
PubMed2004

Clinical evaluation of a computer simulated prediction model of contrast enhancement of the liver in spiral CT.

OBJECTIVE: A software program was developed simulating a compartmental model of blood circulation based on differential equations. The aim of this study was to compare software-simulated levels of hepatic enhancement with the true values in patients and to test how many patients reach the simulated hepatic enhancement level. METHODS: As software program the CT application software carebolus 2 (Siemens, Forchheim, Germany) was used. Hepatic contrast-enhancement curves were simulated prior to CT examinations to evaluate a patient specific time delay after contrast application. At the time delay, when the simulation curve showed an enhancement threshold of 40 Hounsfield Units (HU), the CT spiral scan was started applying 120 ml contrast media with 2 ml/s. The simulated curves were compared with the empiric curves of each patient. RESULTS: 25 of 28 patients (89%) achieved 40 HU. The mean enhancement of empiric patients curves was 46.32 +/- 11.9 HU, the mean simulated enhancement was 46.62 +/- 4.3 HU S.D. (P= 0.48). 4.4 values per patient liver could be compared with the simulation curve (122 points for 28 patients): 50% of the patient curves were within a range of 5 HU compared with the simulation curve. CONCLUSION: Software simulation of contrast enhancement curves of the liver is a feasible and valuable method to predict individual liver enhancement curves. Improvements concerning the integration of cardiovascular parameters and preexisting liver parenchymal diseases into the simulation software have to be arranged.

Adult↗
PubMed2002

Reversible regional wall motion abnormalities on exercise technetium-99m-gated cardiac single photon emission computed tomography predict high-grade angiographic stenoses.

OBJECTIVES: We sought to determine the level of angiographic stenosis at which reversible regional wall motion abnormalities (RWMA) are present on exercise stress technetium-99m (Tc-99m)- gated single photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI), and whether assessments of stress and rest RWMA add incremental diagnostic information. BACKGROUND: Stress and rest gated SPECT MPI enables the detection of post-exercise stunning. Although some studies have correlated RWMA to the severity of MPI defects, only one previous study correlated RWMA on gated MPI to angiographic findings. However, this correlation excluded patients with rest perfusion defects and did not involve gating of rest images. METHODS: One hundred patients undergoing angiography within six months of exercise stress Tc-99m (sestamibi)-gated SPECT MPI (in the absence of interim cardiac events or revascularization) were recruited. Images were acquired 15 to 30 min after stress and interpreted without knowledge of the Duke treadmill score, left ventricular ejection fraction and angiographic data. RESULTS: The sensitivity of reversible RWMA for angiographic stenoses >70% was 53%, with a specificity of 100%. The presence of reversible RWMA was able to stratify patients with angiographic stenoses of 50% to 79% and 80% to 99% with a high positive predictive value. A good correlation was noted between the presence of reversible RWMA and the coronary artery jeopardy score (R = 0.49, p < 0.0001). Multivariate analysis showed that the post-stress RWMA, Duke treadmill and reversible RWMA scores were significant predictors of angiographic severity. CONCLUSIONS: Post-stress and reversible RWMA, as shown by exercise stress Tc-99m-gated SPECT MPI, are significant predictors of angiographic disease and add incremental value to MPI for the assessment of angiographic severity.

Age Factors↗
PubMed2005

MetaCyc and AraCyc. Metabolic pathway databases for plant research.

MetaCyc (http://metacyc.org) contains experimentally determined biochemical pathways to be used as a reference database for metabolism. In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome. To increase the breadth of pathways and enzymes, more than 60 plant-specific pathways have been added or updated in MetaCyc recently. In contrast to MetaCyc, which contains metabolic data for a wide range of organisms, AraCyc is a species-specific database containing only enzymes and pathways found in the model plant Arabidopsis (Arabidopsis thaliana). AraCyc (http://arabidopsis.org/tools/aracyc/) was the first computationally predicted plant metabolism database derived from MetaCyc. Since its initial computational build, AraCyc has been under continued curation to enhance data quality and to increase breadth of pathway coverage. Twenty-eight pathways have been manually curated from the literature recently. Pathway predictions in AraCyc have also been recently updated with the latest functional annotations of Arabidopsis genes that use controlled vocabulary and literature evidence. AraCyc currently features 1,418 unique genes mapped onto 204 pathways with 1,156 literature citations. The Omics Viewer, a user data visualization and analysis tool, allows a list of genes, enzymes, or metabolites with experimental values to be painted on a diagram of the full pathway map of AraCyc. Other recent enhancements to both MetaCyc and AraCyc include implementation of an evidence ontology, which has been used to provide information on data quality, expansion of the secondary metabolism node of the pathway ontology to accommodate curation of secondary metabolic pathways, and enhancement of the cellular component ontology for storing and displaying enzyme and pathway locations within subcellular compartments.

4-Hydroxyphenylpyruvate Dioxygenase↗
PubMed2005

Coronary artery calcification score by multislice computed tomography predicts the outcome of dobutamine cardiovascular magnetic resonance imaging.

The aim of this study was to determine whether a coronary artery calcium (CAC) score of less than 11 can reliably rule out myocardial ischemia detected by dobutamine cardiovascular magnetic resonance imaging (CMR) in patients suspected of having myocardial ischemia. In 114 of 136 consecutive patients clinically suspected of myocardial ischemia with an inconclusive diagnosis of myocardial ischemia, dobutamine CMR was performed and the CAC score was determined. The CAC score was obtained by 16-row multidetector compued tomography (MDCT) and was calculated according to the method of Agatston. The CAC score and the results of the dobutamine CMR were correlated and the positive predictive value (PPV) and the negative predictive value (NPV) of the CAC score for dobutamine CMR were calculated. A total of 114 (87%) of the patients were eligible for this study. There was a significant correlation between the CAC score and dobutamine CMR (p<0.001). Patients with a CAC score of less than 11 showed no signs of inducible ischemia during dobutamine CMR. For a CAC score of less than 101, the NPV and the PPV of the CAC score for the outcome of dobutamine CMR were, respectively, 0.96 and 0.29. In patients with an inconclusive diagnosis of myocardial ischemia a MDCT CAC score of less than 11 reliably rules out myocardial ischemia detected by dobutamine CMR.

Aged↗