Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computational prediction”

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 235 records · Page 13Linked to original sources

A 3-D computational model predicts that cell deformation affects selectin-mediated leukocyte rolling.

Leukocyte recruitment to sites of inflammation is initiated by their tethering and rolling on the activated endothelium under flow. Even though the fast kinetics and high tensile strength of selectin-ligand bonds are primarily responsible for leukocyte rolling, experimental evidence suggests that cellular properties such as cell deformability and microvillus elasticity actively modulate leukocyte rolling behavior. Previous theoretical models either assumed cells as rigid spheres or were limited to two-dimensional representations of deformable cells with deterministic receptor-ligand kinetics, thereby failing to accurately predict leukocyte rolling. We therefore developed a three-dimensional computational model based on the immersed boundary method to predict receptor-mediated rolling of deformable cells in shear flow coupled to a Monte Carlo method simulating the stochastic receptor-ligand interactions. Our model predicts for the first time that the rolling of more compliant cells is relatively smoother and slower compared to cells with stiffer membranes, due to increased cell-substrate contact area. At the molecular level, we show that the average number of bonds per cell as well as per single microvillus decreases with increasing membrane stiffness. Moreover, the average bond lifetime decreases with increasing shear rate and with increasing membrane stiffness, due to higher hydrodynamic force experienced by the cell. Taken together, our model captures the effect of cellular properties on the coupling between hydrodynamic and receptor-ligand bond forces, and successfully explains the stable leukocyte rolling at a wide range of shear rates over that of rigid microspheres.

Biophysics↗

Perfusion computed tomography: prediction of final infarct extent and stroke outcome.

The Alberta Stroke Program Early Computed Tomography Score (ASPECTS) has not been previously applied to perfusion CT (CTP). Five raters assigned ASPECTS to baseline noncontrast CT (NCCT), CT angiography source images (CTA-SI), CTP source images (CTP-SI), and CTP maps of cerebral blood volume (CBV), cerebral blood flow (CBF), and mean transit time (MTT) from 37 consecutive patients with less than 6-hour anterior circulation ischemic stroke. Major reperfusion was identified on follow-up imaging. Mean baseline ASPECTS was compared with follow-up imaging ASPECTS. Rates of favorable outcome were compared for dichotomized baseline ASPECTS. In patients with major reperfusion, mean CBV and CTP-SI ASPECTS closely predicted final infarct ASPECTS. In patients without major reperfusion, mean CBF and MTT ASPECTS best predicted final infarct ASPECTS. There were significant increases in rates of favorable outcome for CTP-SI and CBV ASPECTS of greater than 6, versus less than or equal to 6, but not for other baseline CT modalities. ASPECTS applied to CTP is more accurate at identifying the extent of reversible and irreversible ischemia and at predicting final clinical outcome than NCCTor CTA-SI.

Aged↗

Tumor volume as determined by computed tomography predicts local control in hypopharyngeal squamous cell carcinoma treated with primary surgery.

Computed tomography reliably evaluates hypopharyngeal squamous cell carcinomas (SCC) regarding the infiltration of specific anatomic structures and tumor volumes, both of which have been shown to be predictors of local control in patients treated with radiation therapy alone. However, an association of specific infiltrated structures and/or tumor volume with local control has not been investigated for surgical treatment; thus, we determined relationships of various infiltrated anatomic structures and tumor volume with local control in patients with hypopharyngeal SCC treated with primary surgery. In 45 hypopharyngeal SCC, tumor volumes were measured by pretreatment CT, and extent of tumor infiltration was determined by postoperative pathologic examination. All patients had clinical follow-up for recurrent tumor at the primary site. Statistical analysis basically consisted of chi-square and U-tests. Local control rate was 84.4% (38 of 45). Tumor volume was significantly associated with local control (p=0.004). Six of 16 (38%) patients with tumor volumes > or =8.1 cm3 (mean) had a local recurrence, which is significantly (p=0.003) more compared with 1 of 29 (3%) in the group of patients with volumes <8.1 cm3. Among all evaluated anatomic structures, only a tendency for significant association with local control was found for tumor involvement of the tonsils and the extralaryngeal soft tissues. The determination of tumor volumes by CT helps predict local control in patients with hypopharyngeal SCC treated with primary surgery.

Adult↗

Dynamic computed tomography predicts tumor temperature and response to thermoradiotherapy in superficial and subsurface tumors.

BACKGROUND: Dynamic computed tomography (CT) was performed on patients undergoing thermoradiotherapy for superficial or subsurface tumors, and the correlation between tumor enhancement and tumor temperature during hyperthermia was evaluated. The authors further investigated whether tumor enhancement by dynamic CT is predictive of tumor response to thermoradiotherapy. METHODS: Thermoradiotherapy was given to 26 patients. Radiotherapy consisted of 40-70 gray. Hyperthermia was conducted over 3-5 sessions, and tumor temperature was measured at each session. Dynamic CT was performed prehyperthermia (within 1 week before the initiation of hyperthermia) and midtherapy (within 1 week after 2 sessions of hyperthermia). RESULTS: A complete response (CR) was obtained in 11 patients (42%) and either a partial response or no response (non-CR) in 15 (58%). There was no correlation between tumor enhancement obtained by prehyperthermia CT and tumor temperature parameters or response. However, the deltaCTmax (maximum increased enhancement) by prehyperthermia and midtherapy CT was 39.0 +/- 18.9 HU and 26.1 +/- 14.2 HU, respectively, in CR patients, and 46.4 +/- 21.1 HU and 49.6 +/- 19.1 HU, respectively, in non-CR patients. This change in deltaCTmax at midtherapy was significantly different between groups (P < 0.01). The deltaCTmax ratio for prehyperthermia and midtherapy CT studies correlated with the average tumor temperature (P < 0.05). CONCLUSIONS: Tumor enhancement by prehyperthermia and midtherapy dynamic CT predicted tumor temperature during hyperthermia and response to thermoradiotherapy for superficial or subsurface malignancies.

Adult↗

Computer-aided prediction of gangrenous and perforating appendicitis.

The clinical details of 100 patients with proved acute appendicitis were compared with those of 100 patients with perforating or gangrenous appendicitis. Twenty features were found to be significantly different between the two groups. This information was incorporated into a computer data base and used in the differential diagnosis of abdominal pain. A program written to predict the probability that gangrene or perforation was present in patients with appendicitis gave a diagnostic accuracy over 91%. A clinical scoring index, which accurately predicted the state of the appendix in 88% of patients, was constructed from the significant differences between the two groups. When clinical scoring or computer analysis predicts a high probability of perforation or gangrene in patients with appendicitis, surgery should be performed without delay.

Acute Disease↗

Low pretreatment gallbladder stone densities at computed tomography predict rapid stone clearance following extracorporeal shock wave lithotripsy.

The importance of routine computer tomographic (CT) stone analysis in optimizing the therapeutic outcome after extracorporeal shock wave lithotripsy (ESWL) remains controversial. The aim of the present prospective study was to seek a correlation between CT findings and stone clearance rates after ESWL in 159 patients. One hundred fifty-nine symptomatic patients (116 females, 43 males) with solitary radiolucent gallbladder stones underwent CT for stone analysis before lithotripsy. In Group I (<50 HU, n=104), stone clearance was achieved in 55.8% of patients within 6.11+/- 6.95 months; in Group II (51-100 HU, n = 28), in 50.0% of patients within 11.2 +/- 10.3 months; in Group III (>100 HU, n = 27) in 29.7% of patients within 9.60 +/- 6.96 months. The mean follow-up period was 17.9 +/- 10.0 months. Patients in Group I showed a significantly higher rate of stone clearance than those in Groups II and III (p < 0.001) as well as a significantly shorter time for the achievement of total stone clearance than either of the other groups (p < 0.001). The authors conclude that CT stone analysis provides a more accurate method of selecting patients suitable for ESWL and may be of importance in predicting the expected length of time for achieving complete stone clearance.

Absorptiometry, Photon↗

Studies on the relationship between in vitro metabolism and certain physicochemical characteristics of some 9-alkyl-/9-aralkyl adenines.

Previous studies demonstrated that biological N1-oxidation occurred for some 9-alkyl-/9-aralkyladenines, but not for others, when mammalian hepatic microsomal incubates were used as enzyme source. In order to understand the mechanisms controlling the metabolic fate of these compounds, the relationship between N1-oxidation and certain physicochemical characteristics of these substrates was studied. It was found that there was no marked link between N1-oxidation and the computer predicted pKa values of the substances studied. However, a computer predicted LogP value in the range 1.3-4 seems to be the most favourable for N1-oxidation. The 1H-NMR and 13C-NMR spectroscopic characteristics of the substrates, which reflect certain electronic characteristics of the purine moiety, also showed a correlation with their N1-oxidation. The electronic effects of the substrates in relation to their metabolism was investigated using computer modelling techniques; the results showed that different substituents at the 9-position of adenine may modify the electronic characteristics of the purine moiety thus affecting their metabolism. The conformation of the substrates may also be an important controlling factor for their N1-oxidative metabolism.

Adenine↗

Postfracture instability of vertebrae with simulated defects can be predicted from computed tomography data.

STUDY DESIGN: Structural properties of vertebrae with simulated defects were measured from computed tomography data. Relations between structural properties and postfracture stability were tested using linear regressions. OBJECTIVES: To determine whether the postfracture stability of lumbar and thoracic vertebrae can be predicted from noninvasive, prefracture measurements of structural properties. SUMMARY OF BACKGROUND DATA: Sensitive and specific guidelines are needed that can predict fracture risk and spinal stability after pathologic fractures. Such guidelines may help determine whether treatment is needed to prevent neurologic complications. Simple measurements made from computed tomography data can predict the load-bearing capacity of intact vertebrae and vertebrae with simulated and actual metastatic defects. It is not known whether these same measurements can also predict postfracture stability. METHOD: Simulated metastatic defects were created in human three-vertebrae segments from the lumbar and thoracic spine. Axial rigidity was calculated from quantitative computed tomography data, and failure load and postfracture stability were measured. RESULTS: Postfracture stability was linearly correlated with both failure load (r2 = 0.3-0.6) and axial rigidity (r2 = 0.3-0.6). CONCLUSIONS: The postfracture stability of three-vertebrae segments with simulated defects was modestly related to noninvasively measured, prefracture structural properties.

Adult↗

pTARGET: a web server for predicting protein subcellular localization.

The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963-3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770,000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from http://bioinformatics.albany.edu/~ptarget.

Algorithms↗

Can high resolution computed tomography predict lung function in patients with chronic obstructive pulmonary disease?

High-resolution computed tomography (HRCT) is a useful method for quantifying the extent of emphysema. Few reports have mentioned the relationships between HRCT scans and pulmonary function tests in chronic obstructive pulmonary disease (COPD). For diagnosis, COPD requires chronic airflow limitation and emphysema and/or chronic bronchitis. We examined 20 who were previous smokers with middle to moderate COPD. All were normocapnic with mean arterial oxygen pressure (PaO2) 77,52 +/- 16,789 mmHg. Forced spirometry, somatic plethysmography and cardiopulmonary exercise test were performed in each patient. HRCT was performed in both full inspiration and full expiration at three levels through the upper (at the aortic arch), lower (2 cm above the diaphragm), and middle lung (midpoint between upper and lower) levels. During expiration all pulmonary function parameters correlated with the HRCT grade in the middle right and left part of the lungs. The middle right part of the lung during expiration correlated statistically significant with MVV (r = -0.681, p = 0.001), forced vital capacity (FVC) (r = -0.477, p = 0.027), forced expiratory volumein 1 sec (FEV1) (r = -0.632, p = 0.002), resistance (r = 0.674, p = 0.001), residual volume (RV) (r = 0.733, p = 0.001), total lung capacity (TLC) (r = 0.696, p = 0.001), functional residual capacity (FRC) (r = 0.752, p = 0.001) and peak oxygen consumption during exercise (VO2) (r = -0.493, p = 0.023). The middle left part of the lung during expiration correlated statistically significant with MVV (r = -0.673, p = 0.001), FVC (r = -0.493, p = 0.027), FEV1 (r = -0.629, p = 0.003), resistance (r = 0.593,p = 0.005), RV (r = 0.601, p = 0.005), TLC (r = 0.546, p = 0.012), FRC (r = 0.594, p = 0.006) and peak VO2 (r = -0.525, p = 0.015). Forced expiratory volume in 1 sec (FEV1), which is a well-established measure of airflow obstruction, correlated with the HRCT grade (1) in the middle left part of the lung during inspiration (r = -0.468, p = 0.035) and during expiration (r = - 0.629, p = 0.003) (2) in the lower right lung during inspiration (r = -0.567, p = 0.007) and during expiration (r = -0.558, p = 0.008) (3) in the lower left lung during inspiration (r = -0.542, p = 0.011) and during expiration (r = -0.558, p = 0.008) (4) in the upper right lung during expiration (r = -0.469, p = 0.037) (5) in the upper left lung during expiration (r = -0.463, p = 0.035) and (6) in the middle right lung during expiration (r = -0.632, p = 0.002). According to our results HRCT was a valuable tool for evaluating the severity of COPD--especially the middle right and left part of the lungs, during expiration--and correlated well with pulmonary function tests.

Exercise Test↗

Aortic valve calcification on computed tomography predicts the severity of aortic stenosis.

AIM: Incidental aortic valve calcification is often detected during computed tomography. The aim was to compare the severity of valvular stenosis and calcification in patients with aortic stenosis. MATERIALS AND METHODS: One hundred and fifty-seven patients aged 68+/-11 years (range: 34-85) with aortic valve stenosis underwent multislice helical computed tomography and Doppler echocardiography performed by independent, blinded observers. The aortic valve calcium score was determined using automated computer software calibrated with a phantom. RESULTS: Doppler echocardiography demonstrated a post-valve velocity of 3.45+/-0.66 m/s and a peak gradient of 49+/-11 mmHg. Computed tomography showed excellent reproducibility and the median aortic valve calcium score was 5858 AU (interquartile range, 1555-14,596). The computed tomography aortic valve calcium score positively correlated with the Doppler post-valve velocity and peak gradient (r=0.54, p<0.0001 for both) of the aortic valve. All patients with severe aortic stenosis had a calcium score of >3700 AU. CONCLUSION: Calcification of the aortic valve is closely associated with the severity of aortic stenosis, and heavy calcification suggests the presence of severe aortic stenosis that requires urgent cardiological assessment. Patients with lesser degrees of aortic valve calcification should be screened for aortic stenosis and monitored for disease progression.

Adult↗

Computer boom predicted.

Explore the source record for details and available documents.

Accounts Payable and Receivable↗

Comprehensive life table of computer-assisted predictive mathematical relationship between age and life expectancy, survival probability or death rate in US adults.

A microcomputer program in BASIC for predicting life expectancy by age in US adults was designed. Formulas used in this study were derived from the data reported by the National Center for Health Statistics. A comprehensive life table that shows the relationship between age and death rate, survival probability or life expectancy for each year between 25 and 85 years of age was obtained in this study, using a newly designed computer program for predicting life expectancy by age and the program for survival probability previously published by the author. The comprehensive life table may be useful for clinical evaluation of patients and further helpful for biomedical investigation and epidemiological evaluation of US adults.

Adult↗

Toward a computational tool predicting the stereochemical outcome of asymmetric reactions. 1. Application to Sharpless asymmetric dihydroxylation.

A reliable and computationally tractable protocol directed at the study of the stereochemical outcome of asymmetric reactions and its application to the Sharpless asymmetric dihydroxylation reaction are proposed. This method, based on a genetic algorithm and molecular mechanics, effectively provides qualitative as well as semiquantitative results and explains the origin of the observed enantioselectivity. For instance, the method reliably predicts reversal of selectivity between similar substrates, unexpected isomers, and even enantio- and diastereoisomeric excess with good accuracy. Two binding modes, closely related to those proposed by Sharpless and Corey, are favored. After comparison with Sharpless' mnemonic device, we propose two alternative interpretations.

Journal Article↗

Poor correspondence between predicted and experimental binding of peptides to class I MHC molecules.

Naturally processed peptides presented by class I major histocompatibility complex (MHC) molecules display a characteristic allele specific motif of two or more essential amino acid side chains, the so-called peptide anchor residues, in the context of an 8-10 amino acid long peptide. Knowledge of the peptide binding motif of individual class I MHC molecules permits the selection of potential peptide antigens from proteins of infectious organisms that could induce protective T-cell-mediated immunity. Several methods have been developed for the prediction of potential class I MHC binding peptides. One is based on a simple scanning for the presence of primary peptide anchor residues in the sequence of interest. A more sophisticated technology is the utilization of predictive computer algorithms. Here, we have analyzed the experimental binding of 84 peptides selected on the basis of the presence of peptide binding motifs for individual class I MHC molecules. The actual binding was compared with the results obtained when analyzing the same peptides by two well-known, publicly available computer algorithms. We conclude that there is no strong correlation between actual and predicted binding when using predictive computer algorithms. Furthermore, we found a high number of false-negatives when using a predictive algorithm compared to simple scanning for the presence of primary anchor residues. We conclude that the peptide binding assay remains an important step in the identification of cytotoxic T lymphocyte (CTL) epitopes which can not be substituted by predictive algorithms.

Algorithms↗

Left ventricular size determined by electron beam computed tomography predicts significant coronary artery disease and events.

A novel method in the measurement of left ventricular (LV) area using noncontrast electron beam computed tomography (EBCT) was introduced and studied as a diagnostic and prognostic marker for coronary artery disease. Larger LV area measured by noncontrast EBCT was significantly associated with angiographic coronary disease and was a better predictor of coronary disease events than log calcium score.

Adult↗

Topological analysis of glucosyltransferase GtrV of Shigella flexneri by a dual reporter system and identification of a unique reentrant loop.

Lipopolysaccharide, particularly the O-antigen component, is one of many virulence determinants necessary for Shigella flexneri pathogenesis. O-Antigen modification is mediated by glucosyltransferase genes (gtr) encoded by temperate serotype-converting bacteriophages. The gtrV gene encodes the GtrV glucosyltransferase, an integral membrane protein that catalyzes the transfer of a glucosyl residue via an alpha1,3 linkage to rhamnose II of the O-antigen unit. This mediates conversion of S. flexneri serotype Y to serotype 5a. Analysis of the GtrV amino acid sequence using computer prediction programs indicated that GtrV had 9-11 transmembrane segments. The computer prediction models were tested by genetically fusing C-terminal deletions of GtrV to a dual reporter system composed of alkaline phosphatase and beta-galactosidase. Sandwiched GtrV-PhoA/LacZ fusions were also constructed at predetermined positions. The enzyme activities of cells with the GtrV-PhoA/LacZ fusions and the particular location of the fusions in the gtrV indicated that GtrV has nine transmembrane segments and one large N-terminal periplasmic loop with the N and C termini located on the cytoplasmic and periplasmic sides of the membrane, respectively. The existence of a unique reentrant loop was discovered after transmembrane segment IV, a feature not documented in other bacterial glycosyltransferases. Its potential role in mediating serotype conversion in S. flexneri is discussed.

Alkaline Phosphatase↗