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PubMed2002

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.

MOTIVATION: We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy. RESULTS: The comparisons we performed were as follows. (1) We compared two predictions of the pathway complements of Helicobacter pylori that were computed by an early version of our pathway-prediction algorithm: prediction A used the EcoCyc E. coli pathway DB as the reference database (DB) for prediction, and prediction B used the MetaCyc pathway DB (a superset of EcoCyc) as the reference pathway DB. The MetaCyc-based prediction contained 75% more pathway predictions, but we believe a significant number of those predictions were false positives. (2) We compared two predictions of the pathway complement of H. pylori that used MetaCyc as the reference pathway DB, but that used different algorithms: the original PathoLogic algorithm, and an enhanced version of the algorithm designed to eliminate false-positive pathway predictions. The improved algorithm predicted 30\% fewer metabolic pathways than the original algorithm; all of the eliminated pathways are believed to be false-positive predictions. (3) We compared the 98 pathways predicted by the enhanced algorithm with the results of a manual analysis of the pathways of H. pylori. Results: 40 of the computationally predicted pathways were consistent with the manual analysis, 13 pathways are considered false-positive predictions, and four pathways had partially overlapping topologies. Twenty-six predicted pathways were not mentioned in the manual analysis; we believe these are correct predictions by PathoLogic that were not found by the manual analysis. Five pathways from the manual analysis were not found computationally. Agreement between the computational and manual predictions was good overall, with the computational analysis inferring many pathways that the manual analysis did not identify. Ultimately the manual analysis is also partially speculative, and therefore is not an absolute measure of correctness. The algorithm is designed to err on the side of more false positives to bring more potential pathways to the user's attention. The resulting H. pylori pathway DB is freely available at http://ecocyc.org:1555/HPY/organism-summary?object=HPY. AVAILABILITY: The Pathway Tools software is freely available to academic users, and is available to commercial users for a fee. Contact pkarp@ai.sri.com for information on obtaining the software.

Algorithms↗

PubMed1994

Predictive value of computed tomography-based diagnosis of intracranial tuberculomas.

The need to obtain histological diagnoses of intracranial tuberculomas, before initiating therapy, is not universally accepted, because some clinicians believe that an image-based diagnosis is fairly accurate in patients from endemic regions. To evaluate the sensitivity, specificity, and predictive value of computed tomography (CT)-based diagnosis of an intracranial tuberculoma, we prospectively compared the preoperative imaging diagnoses with histological diagnoses in 105 consecutive patients with intracranial masses. CT differential diagnoses (first or second) of tuberculomas were considered in 21 patients. Seven of them were histologically confirmed to have tuberculomas (true-positive results); 14 had other diseases (false-positive results). The 14 false-positive cases included 6 cases of astrocytomas, 5 of metastases, and 3 with miscellaneous diagnoses. All tuberculomas were correctly diagnosed on the CT scans (5 by both surgeons and 2 by one surgeon). During the study period, we encountered 11 patients who were referred by other clinicians with diagnoses of tuberculomas on the basis of their CT scans. We concurred with their CT diagnoses in 5 of them, but only 1 patient had a histologically verified tuberculoma. Astrocytomas (4 patients), metastases (3 patients), and solitary cysticercus granulomas (3 patients) were the causes of misdiagnosis in this group of patients. Although the sensitivity of CT in the diagnosis of intracranial tuberculomas is 100%, and its specificity is 85.7%, the positive predictive value is only 33% (confidence limits, 24-42%). The negative predictive value is 100%. The low positive predictive value for a diagnosis of intracranial tuberculoma on CT alone indicates the need for a confirming histological diagnosis.

Adolescent↗

PubMed2005

Computer-aided disease prediction system: development of application software with SAS component language.

AIMS: The intricacy of predictive models associated with prognosis and risk classification of disease often discourages medical personnel who are interested in this field. The aim of this study was therefore to develop a computer-aided disease prediction model underpinning a step-by-step statistics-guided approach including five components: (1) data management; (2) exploratory analysis; (3) type of predictive model; (4) model verification; (5) interactive mode of disease prediction using SAS 8.02 Windows 2000 as a platform. METHODS: The application of this system was illustrated by using data from the Swedish Two-County Trial on breast cancer screening. The effects of tumour size, node status, and histological grade on breast cancer death using logistic regression model or survival models were predicted. A total of 20 questions were designed to exemplify the usefulness of each component. We also evaluated the system using a controlled randomized trial. Times to finish the above 20 questions were used as endpoint to evaluate the performance of the current system. User satisfaction with the current system such as easy to use, the efficiency of risk prediction, and the reduction of barrier to predictive model was also evaluated. RESULTS: The intervention group not only performed more efficiently than the control group but also satisfied with this application software. CONCLUSIONS: The MD-DP-SOS system characterized by menu-driven style, comprehensiveness, accuracy and adequacy assessment, and interactive mode of disease prediction is helpful for medical personnel who are involved in disease prediction.

Decision Support Techniques↗

PubMed1978

Computer method for predicting the secondary structure of single-stranded RNA.

We present a computer method utilizing published values for base pairing energies to compute the most energetically favorable secondary structure of an RNA from its primary nucleotide sequence. After listing all possible double-helical regions, every pair of mutally incompatible regions (whose nucleotides overlap) is examined to determine whether parts of those two regions can be combined by branch migration to form a pair of compatible new subregions which together are more stable than either of the original regions separately. These subregions are added to the list of base pairing regions which will compete to form the best overall structure. Then, a 'hyperstructure matrix' is generated, containing the unique topological relationship between every pair of regions. We have shown that the best structure can be chosen directly from this matrix, without the necessity of creating and examing every possible secondary structure. We have included the results from our solution of the 5S rRNA of the cyanobacterium Anacystis nidulans as an example of our program's capabilities.

Base Sequence↗

PubMed2003

Clinical value of iodine-123 beta-methyliodophenyl pentadecanoic acid (BMIPP) myocardial single photon emission computed tomography for predicting cardiac death among patients with chronic heart failure.

In the present study, the effectiveness of 123I-beta-methyliodophenyl pentadecanoic acid (BMIPP) single photon emission computed tomography (SPECT) for predicting cardiac death of patients with chronic heart failure was evaluated. Abnormalities of fatty acid metabolism are found in patients with chronic heart failure and BMIPP was developed as a tracer for scintigraphic assessment of myocardial fatty acid utilization. The study group comprised 74 patients with chronic heart failure with a left ventricular ejection fraction (LVEF) <45% on left ventriculography or radionuclide angiocardiography. They underwent both 201Tl SPECT and BMIPP SPECT. The uptake of tracer was scored semiquantitatively from 0 (normal) to 4 (defect) in 20 segments and a total defect score (TDS) for all 20 segments was calculated. On planar images the mediastinum to heart count ratio (H/M) was calculated for the BMIPP and Tl studies, and the H/M(BMIPP):H/M(Tl) (H/M(BMIPP) divided by H/M(Tl)) was also calculated. The mean follow-up period was 660 days and there were 17 cases of cardiac death. Multivariate analysis identified H/M(BMIPP):H/M(Tl) (p<0.05) and LVEF (p<0.05) as independent predictors of cardiac death. The receiver-operating characteristic curve of H/M(BMIPP):H/M (Tl) was situated to the left relative to LVEF. Analysis of the myocardial metabolism by BMIPP SPECT can predict the high-risk patients with chronic heart failure.

Aged↗

PubMed2006

Breath-hold single-photon emission tomography and computed tomography for predicting residual pulmonary function in patients with lung cancer.

OBJECTIVE: We sought to evaluate the utility of integrated breath-hold single-photon emission tomography and computed tomography imaging compared with that of simple calculation with the lung segment-counting technique for predicting residual pulmonary function in patients undergoing surgical intervention for lung cancer. METHODS: A prospective series of 22 patients undergoing anatomic lung resection for cancer were enrolled in this study. Postoperative residual forced expiratory volume in 1 second was predicted by measuring the radioactivity counts of the affected lobes or segments to be resected within the entire lungs by placement of regions of interest on single-photon emission tomography and computed tomography images. Residual forced expiratory volume in 1 second was also estimated by using the segment-counting technique. RESULTS: Both predicted values agreed well with postoperative forced expiratory volume in 1 second. Although the residual forced expiratory volume in 1 second predicted by means of single-photon emission tomography and computed tomography correlated well with that predicted by using segment counting, the values were significantly underestimated by the segment-counting technique in 4 outliers with severe emphysema. There were 2 patients with borderline pulmonary functional reserve whose residual forced expiratory volume in 1 second values were predicted more accurately by means of single-photon emission tomography and computed tomography than by using segment counting. CONCLUSION: Integrated breath-hold single-photon emission tomography and computed tomography images allow the accurate prediction of postoperative pulmonary function but without statistical superiority over the simple segment-counting technique. Further study of the usefulness of single-photon emission tomography and computed tomography in patients with severe emphysema and borderline lung function should prove valuable because the segment-counting technique underestimates pulmonary functional reserve in these patients.

Aged↗

PubMed1997

PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices.

MOTIVATION: A large number of new DNA sequences with virtually unknown functions are generated as the Human Genome Project progresses. Therefore, it is essential to develop computer algorithms that can predict the functionality of DNA segments according to their primary sequences, including algorithms that can predict promoters. Although several promoter-predicting algorithms are available, they have high false-positive detections and the rate of promoter detection needs to be improved further. RESULTS: In this research, PromFD, a computer program to recognize vertebrate RNA polymerase II promoters, has been developed. Both vertebrate promoters and non-promoter sequences are used in the analysis. The promoters are obtained from the Eukaryotic Promoter Database. Promoters are divided into a training set and a test set. Non-promoter sequences are obtained from the GenBank sequence databank, and are also divided into a training set and a test set. The first step is to search out, among all possible permutations, patterns of strings 5-10 bp long, that are significantly over-represented in the promoter set. The program also searches IMD (Information Matrix Database) matrices that have a significantly higher presence in the promoter set. The results of the searches are stored in the PromFD database, and the program PromFD scores input DNA sequences according to their content of the database entries. PromFD predicts promoters-their locations and the location of potential TATA boxes, if found. The program can detect 71% of promoters in the training set with a false-positive rate of under 1 in every 13,000 bp, and 47% of promoters in the test set with a false-positive rate of under 1 in every 9800 bp. PromFD uses a new approach and its false-positive identification rate is better compared with other available promoter recognition algorithms. The source code for PromFD is in the 'c+2' language.

Algorithms↗

PubMed1984

Computer simulation to predict patient responses to alterations in the ventilation regime.

We have developed a technique for simulating artificially ventilated patients using a computer model of the respiratory system and have investigated its ability to predict the patient's response to alterations in the ventilation regime. The majority of those studied were in a stable condition following cardiac surgery. Predictions for PaO2 showed a reasonable correlation with measured values (r = 0.94), although individual predictions could differ appreciably (SEE = +/- 17.3 mmHg). Predictions for PaCO2 correlated less well (r = 0.89, SEE = +/- 2.0 mmHg) and there was a consistent tendency to overestimate this variable. The least accurate predictions were those for PvO2 (r = 0.61, SEE = +/- 3.8 mmHg). Errors in prediction were attributable to deficiencies in the model (most importantly the three-compartment lung and the modelling of CO2 production, storage and excretion), compounded by unpredictable alterations in the patient's physiology (mainly Vo2, Vco2 and Qt). However, allowing for accepted clinical variability and routine measurement accuracy, the predictions are generally reasonable. This suggests that, with some further modifications, computer modelling of this, and other, systems may prove to be a clinically and educationally useful technique.

Adult↗

PubMed1988

BIGPROBE: a computer program that predicts the sequence of long oligonucleotide probes with high reliability.

We have written a computer program, BIGPROBE, which facilitates the design of long nucleic acid probes from the partial or complete amino acid sequence of a protein. BIGPROBE relies upon information on codon usage, intercodon dinucleotide frequency, and potential probe self-complementarity. We have examined the accuracy with which the program predicts coding sequences using sample human and rat genes and probe lengths of 30-60 nucleotides. Rat probe sequences selected by BIGPROBE using either codon usage or dinucleotide frequency data alone averaged 86-92% homology with the known exons of the corresponding gene sequences. Predictive accuracy with rat gene probes could be improved to 89-94%, depending upon probe length, by applying codon usage and dinucleotide frequency data in combination. Similar accuracy was achieved for human genes.

Amino Acid Sequence↗

PubMed2005

Computational fluid dynamic prediction of the residence time of a vortex separator applied to disinfection.

A Hydrodynamic Vortex Separator (HDVS) has been modelled using Computational Fluid Dynamics (CFD) in order to predict the residence time of the fluid at the overflow and underflow outlets. A technique which was developed for use in Heating, Ventilation and Air Conditioning (HVAC) was used to determine the residence time and the results have been compared with those determined experimentally. It is shown that in using CFD, it is possible to predict the mean residence time of the fluid and to study the response to a pulse injection of tracer. It is also shown that it is possible to apply these techniques to predict the mean survival rate of bacteria in a combined separation and disinfection process.

Bacteria↗

PubMed2006

Towards predictive ligand design with free-energy based computational methods?

The accurate prediction of ligand-biopolymer binding affinities is of general interest to medicinal chemistry, as well as to the broader field of molecular recognition. The ability to predict computationally the thermodynamics of these molecular recognition processes has been relatively weak until recently, however, continued developments on several fronts are extending the scope of applicability of these methods. The rapid growth in the number of protein-ligand structures has initially led to the development of a range of empirical scoring functions based on relatively simple descriptions of intermolecular interactions. These methods have had some success in ranking binding affinities when tuned to particular protein systems or in rather qualitative estimates of molecular fit in fast docking calculations. However, they are too unreliable for more detailed, quantitative, assessment and comparison of binding affinities. Physics-based free energy calculations are in principle more general and have the potential to be significantly more accurate. These approaches have seen steady development over many years and rely on carefully calibrated molecular energy functions (force-fields), simulations of the systems with explicit solvent, and the coming-of-age of continuum solvation models. In addition to the initially developped Free Energy Perturbation (FEP) and Thermodynamic Integration (TI) methods, new approaches include the Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) and the Linear Interaction Energy (LIE) approaches. This review concentrates on MM-PBSA and LIE, and their variants. The routine application of these calculations is becoming possible because of enhanced computational hardware and the development of a range of computational chemistry tools. This review addresses: i) the basic principles behind free energy calculations ii) recent methodological advances iii) comparisons of predicted and experimentally determined affinities iv) the uncertainties and limitations of both the computational and experimental data v) areas where progress can be made vi) the practicality of applying the methods at the different stages of the drug discovery and optimization process.

Animals↗

PubMed2002

Semiquantitative dynamic computed tomography to predict response to anti-platelet therapy in acute cerebral infarction.

We investigated whether dynamic computed tomography (CT) in patients with acute cerebral infarction could identify patients likely to respond to anti-platelet therapy. Seventy patients underwent semiquantitative dynamic CT within 6 h as well as cerebral angiography. All then received anti-platelet therapy with a thromboxane A2 synthetase inhibitor. Peak value (pv) and time-to-peak (tp) (time-density curves) for the Sylvian fissure were extracted from dynamic CT data and standardizing interpatient data, two indices, PV/TP index and TP index, were prepared following a standard semiquantitative manner. Both PV/TP index and TP index were effective in discriminating between 48 responders (modified Rankin scale (mRS): 0 to 2) and 22 non-responders (mRS: 3 to 5, or death: 6; both P<0.0001). High PV/TP index (>or=0.8) was a strong indicator of favorable response. Most of these patients maintained regional cerebral blood flow (rCBF) via anterograde flow or collaterals, with a TP index 1.1) and non-compensated rCBF. Intermediate PV/TP values could not predict outcome. Dynamic CT prior to therapy can identify patients with acute cerebral infarction who are treatable with anti-platelet therapy alone.

Acute Disease↗

PubMed1996

Early localization of necrosis by contrast-enhanced computed tomography can predict outcome in severe acute pancreatitis.

A total of 161 primary contrast-enhanced computed tomography (CT) scans of patients with acute necrotizing pancreatitis taken between 1982 and 1994 were analysed retrospectively. The aim was to assess the prognostic significance of the extent and anatomical site of pancreatic tissue necrosis in the first contrast-enhanced CT scan. The scans were obtained a mean of 2.9 days after the onset of symptoms. The pancreatic head was affected in 107 patients, the body in 119 and the tail in 138. Pancreatic tissue necrosis, when divided into four groups according to anatomical site, correlated with overall clinical outcome. The anatomical site of necrosis was clearly better than its crude extent in predicting the risk of complications. For patients with necrosis in the head of the pancreas, the outcome was as severe as when the entire pancreas was affected. In contrast, for patients with necrosis only in the distal part of the pancreas, the outcome was favourable with few complications. The exact site of pancreatic tissue necrosis should be known when early contrast-enhanced CT is used in prognostic scoring.

Acute Disease↗

PubMed2005

Diagnostic utility of positron emission tomography-computed tomography for predicting malignancy in cystic neck masses in adults.

OBJECTIVES: Combined positron emission tomography and computed tomography (PET-CT) is used for the diagnostic evaluation and staging of squamous cell carcinoma of the head and neck (SCCHN). By superimposing anatomic localization of CT with the physiologic data of PET, occult primary and metastatic neoplasms might be identified. Because the diagnostic algorithm for cystic neck masses in adults often overlaps with the work-up of cancer of unknown primary site, we evaluated the utility of PET-CT scans to identify the presence of malignancy and the location of primary tumor. STUDY DESIGN: Single-institution retrospective case review series. METHODS: We reviewed the PET-CT imaging of cystic neck masses occurring in five patients over 40 years of age with significant risk factors for SCCHN and correlated this information with histopathology. RESULTS: In each patient in our series, the PET portion of a combined PET-CT was misleading, whereas the CT examination was more suggestive of the correct pathology. Ultimately, clinical judgment and endoscopic evaluation, guided by CT findings, were most valuable for distinguishing malignant versus benign processes and identifying the primary tumor sites. CONCLUSIONS: PET-CT may not be a reliable modality for identifying malignancy in adults with suspicious cystic neck masses. A thorough clinical evaluation by an experienced head and neck surgeon, in conjunction with contrast-enhanced CT, may be sufficient to facilitate the optimal management of such patients.

Adult↗

PubMed2003

Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases.

Modular polyketide synthases (PKSs) are large multi-enzymatic, multi-domain megasynthases, which are involved in the biosynthesis of a class of pharmaceutically important natural products, namely polyketides. These enzymes harbor a set of repetitive active sites termed modules and the domains present in each module dictate the chemical moiety that would add to a growing polyketide chain. This modular logic of biosynthesis has been exploited with reasonable success to produce several novel compounds by genetic manipulation. However, for harnessing their vast potential of combinatorial biosynthesis, it is essential to develop knowledge based in silico approaches for correlating the sequence and domain organization of PKSs to their polyketide products. In this work, we have carried out extensive sequence analysis of experimentally characterized PKS clusters to develop an automated computational protocol for unambiguous identification of various PKS domains in a polypeptide sequence. A structure based approach has been used to identify the putative active site residues of acyltransferase (AT) domains, which control the specificities for various starter and extender units during polyketide biosynthesis. On the basis of the analysis of the active site residues and molecular modelling of substrates in the active site of representative AT domains, we have identified a crucial residue that is likely to play a major role in discriminating between malonate and methylmalonate during selection of extender groups by this domain. Structural modelling has also explained the experimentally observed chiral preference of AT domain in substrate selection. This computational protocol has been used to predict the domain organization and substrate specificity for PKS clusters from various microbial genomes. The results of our analysis as well as the computational tools for prediction of domain organization and substrate specificity have been organized in the form of a searchable computerized database (PKSDB). PKSDB would serve as a valuable tool for identification of polyketide products biosynthesized by uncharacterized PKS clusters. This database can also provide guidelines for rational design of experiments to engineer novel polyketides.

Amino Acid Sequence↗

PubMed2000

New look at endometrial echogenicity: objective computer-assisted measurements predict endometrial receptivity in in vitro fertilization-embryo transfer.

OBJECTIVE: To determine whether endometrial echogenicity, assessed objectively by a computer-assisted system on the day of hCG administration, predicts endometrial receptivity in controlled ovarian hyperstimulation (COH) cycles for IVF-ET. DESIGN: Prospective analysis. SETTING: Assisted reproduction unit, Clamart, France. PATIENT(S): Two hundred twenty-one women (aged <38 years with a normal uterus and >/=2 grade A or B embryos transferred) undergoing 228 GnRH agonist and FSH/hCG cycles for IVF-ET. INTERVENTION(S): On the day of hCG administration, uterine ultrasound scans were digitized with an image analysis system. Endometrial echogenicity was assessed as the ratio of the extent of the hyperechogenic transformation over the whole endometrial thickness. According to this, cycles were sorted arbitrarily into six groups: <30% (n = 34), 31%-40% (n = 37), 41%-50% (n = 37), 51%-60% (n = 55), 61%-70% (n = 37), and >70% (n = 28). MAIN OUTCOME MEASURE(S): Pregnancy and implantation rates. RESULT(S): The groups were similar in regard to population characteristics, ovarian response to COH, and embryology data. Pregnancy rates (59%, 57%, 35%, 20%, 16%, and 11%, respectively) and implantation rates (35%, 23%, 17%, 6%, 7%, and 3%, respectively) fell progressively and significantly from the low-echogenicity group to the high-echogenicity group. CONCLUSION(S): The present results confirm and extend previous observations that advanced hyperechogenic transformation of the endometrium is associated with poor IVF-ET outcome.

Adult↗

PubMed2006

Aberrant 3' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

The frequency distribution of mutation-induced aberrant 3' splice sites (3'ss) in exons and introns is more complex than for 5' splice sites, largely owing to sequence constraints upstream of intron/exon boundaries. As a result, prediction of their localization remains a challenging task. Here, nucleotide sequences of previously reported 218 aberrant 3'ss activated by disease-causing mutations in 131 human genes were compared with their authentic counterparts using currently available splice site prediction tools. Each tested algorithm distinguished authentic 3'ss from cryptic sites more effectively than from de novo sites. The best discrimination between aberrant and authentic 3'ss was achieved by the maximum entropy model. Almost one half of aberrant 3'ss was activated by AG-creating mutations and approximately 95% of the newly created AGs were selected in vivo. The overall nucleotide structure upstream of aberrant 3'ss was characterized by higher purine content than for authentic sites, particularly in position -3, that may be compensated by more stringent requirements for positive and negative nucleotide signatures centred around position -11. A newly developed online database of aberrant 3'ss will facilitate identification of splicing mutations in a gene or phenotype of interest and future optimization of splice site prediction tools.

Algorithms↗

PubMed2001

Coronary artery calcium determined by electron beam computed tomography for predicting angiographic coronary artery disease in moderate- to high-risk Chinese patients.

The aim of this study was to evaluate the prevalence of coronary calcification among moderate- to high-risk Chinese patients and to evaluate the ability of the coronary calcium score determined by electron beam computed tomography (EBCT) to predict angiographic coronary artery disease in this population. We enrolled 163 consecutive patients and analyzed their cardiovascular risk factors, coronary calcium scores and coronary angiogram results. One hundred and twenty-five patients (76.7%) had a positive EBCT scan result (coronary calcium score >0). The prevalence of calcification and the calcium scores showed a graded relation to the number of cardiovascular risk factors and age (p < 0.001 for trend). Coronary calcium scores showed statistically significant differences between patients with angiographic evidence of coronary artery disease and patients with normal coronary angiography (p < 0.05), but could not differentiate between patients with significant and insignificant coronary artery disease. Receiver operating characteristic curve analysis showed that a coronary calcium score >5 predicted angiographic coronary artery disease with 93% sensitivity and 86% specificity (area under the curve 0.95 +/- 0.019). Multivariate analysis showed a coronary calcium score >5 to be the strongest independent predictor of angiographic coronary artery disease (odds ratio 120.7, 95% confidence interval 21.7-671.4; p < 0.001). Coronary calcium score determined by EBCT appears to have a similar predictive value in Chinese patients as it does in other ethnic populations that have been reported to date.

Adult↗