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At least 487 records · Page 27Linked to original sources
PubMed1994

Midplane dose determination using in vivo dose measurements in combination with portal imaging.

The possibility of using portal films in combination with semiconductor in vivo measurements for midplane dose distribution is investigated. A general algorithm, using measured entrance and exit doses and available beam data of the Linac, is proposed to derive the midplane dose for symmetrical inhomogeneities. Experimental verification of the algorithm with phantom measurements is performed for different kinds of inhomogeneities (Al, air and cork) and phantom thicknesses from 13 cm to 30 cm. When using only the entrance dose and the exit dose, provided by the diodes on the beam axis, the algorithm predicts for the different inhomogeneities midplane doses in all cases within 1% of the midplane doses measured with an ionization chamber. When using the portal film in combination with entrance and exit dose measurements to estimate the midplane dose in an off-axis position, the calculated midplane doses are within 3% of the midplane doses measured with an ionization chamber. The midplane doses calculated with the algorithm are compared to the midplane doses obtained with simplified calculation methods, i.e. the arithmetical mean and the geometrical mean of the measured entrance and exit doses. The geometrical mean especially seems to give acceptable results (within 5%) and can as such be used as an easy rule of thumb to estimate roughly the midplane dose. Finally, critical considerations on the validity and the precision of the proposed algorithm are given. The present results confirm the possibility of using the portal film for midplane dose distribution determination at the patient level.

Algorithms↗
PubMed2002

Noninvasive total hemoglobin measurement.

Wavelength selection and prediction algorithm for determining total hemoglobin concentration are investigated. A model based on the difference in optical density induced by the pulsation of the heart beat is developed by taking an approximation of Twersky's theory on the assumption that the variation of blood vessel size is small during arterial pulsing. A device is constructed with a five-wavelength light emitting diode array as the light source. The selected wavelengths are two isobestic points and three in compensation for tissue scattering. Data are collected from 129 outpatients who are randomly grouped as calibration and prediction sets. The ratio of the variations of optical density between systole and diastole at two different wavelengths is used as a variable. We selected several such variables that show high reproducibility among all variables. Multiple linear regression analysis is made in order to predict total hemoglobin concentration. The correlation coefficient is 0.804 and the standard deviation is 0.864 g/dL for the calibration set. The relative percent error and standard deviation of the prediction set are 8.5% and 1.142 g/dL, respectively. We successfully demonstrate the possibility of noninvasive hemoglobin measurement, particularly, using the wavelengths below 1000 nm.

Algorithms↗
PubMed1999

Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps.

Broad-specificity efflux pumps have been implicated in multidrug-resistant strains of Pseudomonas aeruginosa and other Gram-negative bacteria. Most Gram-negative pumps of clinical relevance have three components, an inner membrane transporter, an outer membrane channel protein, and a periplasmic protein, which together coordinate efflux from the cytoplasmic membrane across the outer membrane through an unknown mechanism. The periplasmic efflux proteins (PEPs) and outer membrane efflux proteins (OEPs) are not obviously related to proteins of known structure, and understanding the structure and function of these proteins has been hindered by the difficulty of obtaining reasonable multiple alignments. We present a general strategy for the alignment and structure prediction of protein families with low mutual sequence similarity using the PEP and OEP families as detailed examples. Gibbs sampling, hidden Markov models, and other analysis techniques were used to locate motifs, generate multiple alignments, and assign PEP or OEP function to hypothetical proteins in several species. We also developed an automated procedure which combines multiple alignments with structure prediction algorithms in order to identify conserved structural features in protein families. This process was used to identify a probable alpha-helical hairpin in the PEP family and was applied to the detection of transmembrane beta-strands in OEPs. We also show that all OEPs contain a large tandem duplication, and demonstrate that the OEP family is unlikely to adopt a porin fold, in contrast to previous predictions.

Amino Acid Sequence↗
PubMed1988

Use of synthetic peptides to map the antigenic determinants of glycoprotein D of herpes simplex virus.

The predictive algorithm Surfaceplot (J.M.R. Parker, D. Guo, and R.S. Hodges, Biochemistry 25:5425-5432, 1986) was used to examine glycoprotein D of herpes simplex virus type 1 (HSV-1) for amino acid residues with a high probability of being exposed on the molecular surface. Based on these data, 11 different peptides corresponding to 10-residue segments in the primary sequence of glycoprotein D and one 20-residue segment were synthesized, conjugated to carrier proteins, and used to generate specific antisera in rabbits. Two synthetic peptides predicted not to be on the surface of glycoprotein D were included as negative controls. The polyclonal antisera against individual synthetic peptide conjugates were in turn evaluated for their ability to recognize both isolated glycoprotein D and intact HSV-1 virions in an enzyme-linked immunosorbent assay. Based on Surfaceplot predictions, eight linear antigenic sites on glycoprotein D were thereby defined from the 12 antipeptide antisera prepared. Four of these sites contained epitopes to which complement-independent neutralizing antibodies could be generated. The latter sites corresponded to sequences 12 to 21, 267 to 276, 288 to 297, and 314 to 323 of the mature protein. An additional peptide sequence, 2 to 21, was found to generate antisera which had potent virus-neutralizing capacity in the presence of complement. Identification of a neutralizing epitope in the sequence 314 to 323 makes it likely that the membrane-spanning region of glycoprotein D is within the subsequent sequence, 323 to 339. Antipeptide antisera prepared in this study from 12 synthetic peptides contained 13 surface sites predicted by Surfaceplot, of which 7 were not predicted by the parameters of Hopp and Woods (Proc. Natl. Acad. Sci. USA 78:3824-3828, 1981). Of these seven sites not predicted by the Hopp and Woods plot, all generated antipeptide antibodies that bound to HSV-1 virions and three of these seven sites generated neutralizing antibodies. In total, 8 of 12 synthetic peptides containing surface regions produced antipeptide antibodies that bound to HSV-1 virions and 5 of these generated neutralizing antibodies. These results suggest the advantages of Surfaceplot in mapping antigenic determinants in proteins.

Algorithms↗
PubMed1995

Prediction of protein structural classes.

A protein is usually classified into one of the following five structural classes: alpha, beta, alpha + beta, alpha/beta, and zeta (irregular). The structural class of a protein is correlated with its amino acid composition. However, given the amino acid composition of a protein, how may one predict its structural class? Various efforts have been made in addressing this problem. This review addresses the progress in this field, with the focus on the state of the art, which is featured by a novel prediction algorithm and a recently developed database. The novel algorithm is characterized by a covariance matrix that takes into account the coupling effect among different amino acid components of a protein. The new database was established based on the requirement that the classes should have (1) as many nonhomologous structures as possible, (2) good quality structure, and (3) typical or distinguishable features for each of the structural classes concerned. The very high success rate for both the training-set proteins and the testing-set proteins, which has been further validated by a simulated analysis and a jackknife analysis, indicates that it is possible to predict the structural class of a protein according to its amino acid composition if an ideal and complete database can be established. It also suggests that the overall fold of a protein is basically determined by its amino acid composition.

Algorithms↗
PubMed2001

High-sensitivity C-reactive protein: potential adjunct for global risk assessment in the primary prevention of cardiovascular disease.

Inflammation plays a major role in atherothrombosis, and measurement of inflammatory markers such as high-sensitivity C-reactive protein (HSCRP) may provide a novel method for detecting individuals at high risk of plaque rupture. Several large-scale prospective studies demonstrate that HSCRP is a strong independent predictor of future myocardial infarction and stroke among apparently healthy men and women and that the addition of HSCRP to standard lipid screening may improve global risk prediction among those with high as well as low cholesterol levels. Because agents such as aspirin and statins seem to attenuate inflammatory risk, HSCRP may also have utility in targeting proven therapies for primary prevention. Inexpensive commercial assays for HSCRP are now available; they have shown variability and classification accuracy similar to that of cholesterol screening. Risk prediction algorithms using a simple quintile approach to HSCRP evaluation have been developed for outpatient use. Thus, although limitations inherent to inflammatory screening remain, available data suggest that HSCRP has the potential to play an important role as an adjunct for global risk assessment in the primary prevention of cardiovascular disease.

Algorithms↗
PubMed1997

A volumetric study of measurements and calculations of lung density corrections for 6 and 18 MV photons.

PURPOSE: For treatment of lung cancer, dose heterogeneity corrections and subsequent prescription alteration remain controversial. Previous dosimetry studies based on slab geometry with a single beam geometry do not represent the clinical situation. A circumscribed tumor within lung poses a more complex problem. Energy choice also remains controversial. METHODS AND MATERIALS: An anthropomorphic phantom was modified by replacing lung cylinders (2.5 and 5.0 cm diameters by 5.0 cm length) with muscle-equivalent cylinders. The phantom was scanned on a CT simulator. Gross, clinical, and planning target volumes (GTV, CTV, PTV1 including tumor and regional nodes, PTV2 including tumor only) were designated slice-by-slice. Three-dimensional planning was performed with large fields (AP/PA/RPO) covering PTV1 and boost fields optimized for each PTV2, for 6 and 18 MV photons. Homogeneous, Ratio-Tissue-Air-Ratio (RTAR), and convolution-adapted RTAR (CARTAR) calculation algorithms were tested. Film was placed between phantom slices at the "tumor" levels. The phantom was irradiated with monitor units corresponding to homogeneous calculations, based on a homogeneous prescription. Measured and calculated doses were compared by isodoses and dose volume histograms. Ionization chambers and TLDs were also used for some test cases. RESULTS: The measured minimum dose covering PTV2 was within 5% of the homogeneous prescription dose of 70 Gy for 6 MV photons, while a lower dose (89% of prescription dose) was measured for 18 MV. The algorithms overpredicted the minimum dose to PTV2 by 6-18%. If the monitor units had been reduced according to simplistic heterogeneous calculations, the small PTV2 would have only been covered by 58 Gy for 18 MV irradiation. Based on this, a clinician may opt to actually increase the prescribed dose, thereby offsetting decreased monitor units. None of the algorithms predicted the diffuse penumbra associated with 18 MV photons in lung. CONCLUSION: Before adjusting dose prescriptions based on heterogeneity corrections, realistic phantom studies must be performed. The accuracy and effect of the corrections must then be assessed. The deficient coverage of PTV2 by the 18 MV beam compares unfavorably with the slight increase (5%) in hot spots associated with 6 MV. Our studies support strong caution before reducing dose prescriptions based on simple algorithms.

Algorithms↗
PubMed1985

Preliminary identification of the secondary structure of the trp repressor from Escherichia coli.

The probable secondary structure content of the trp repressor from Escherichia coli has been inferred from NMR and circular dichroic measurements; the results are compared with those of prediction algorithms. 70% of the amide protons have exchange rate constants orders of magnitude smaller than the intrinsic rate constants, identifying them as participating in hydrogen bonds. The exchange rate constants fall into two distinct classes, one having half-lives of 20 min and the other more than 24 h. The latter class, consisting of 50% of all amide protons, indicates a stable core. The exchange data are consistent with circular dichroism and predictions that suggest that about 55% of the peptides from alpha helix, and 20% form beta sheets and turns. The NMR spectrum further indicates that there is little beta sheet, suggesting that the secondary structure class is alpha.

Amides↗
PubMed2003

Transition from natively unfolded to folded state induced by desiccation in an anhydrobiotic nematode protein.

Late embryogenesis abundant (LEA) proteins are associated with desiccation tolerance in resurrection plants and in plant seeds, and the recent discovery of a dehydration-induced Group 3 LEA-like gene in the nematode Aphelenchus avenae suggests a similar association in anhydrobiotic animals. Despite their importance, little is known about the structure of Group 3 LEA proteins, although computer modeling and secondary structure algorithms predict a largely alpha-helical monomer that forms coiled coil oligomers. We have therefore investigated the structure of the nematode protein, AavLEA1, in the first such analysis of a well characterized Group 3 LEA-like protein. Immunoblotting and subunit cross-linking experiments demonstrate limited oligomerization of AavLEA1, but analytical ultracentrifugation and gel filtration show that the vast majority of the protein is monomeric. Moreover, CD, fluorescence emission, and Fourier transform-infrared spectroscopy indicate an unstructured conformation for the nematode protein. Therefore, in solution, no evidence was found to support structure predictions; instead, AavLEA1 seems to be natively unfolded with a high degree of hydration and low compactness. Such proteins can, however, be induced to fold into more rigid structures by partner molecules or by altered physiological conditions. Because AavLEA1 is associated with desiccation stress, its Fourier transform-infrared spectrum in the dehydrated state was examined. A dramatic but reversible increase in alpha-helix and, possibly, coiled coil formation was observed on drying, indicating that computer predictions of secondary structure may be correct for the solid state. This unusual finding offers the possibility that structural shifts in Group 3 LEA proteins occur on dehydration, perhaps consistent with their role in anhydrobiosis.

Algorithms↗
PubMed1991

An updated comparison of drug dosing methods. Part II: Theophylline.

This article updates the previous review in the Journal regarding theophylline dosing methods. Among the predictive algorithms evaluated, the dose-titration scheme of Weinberger and Hendeles was extensively tested in 1073 asthmatic patients. When the scheme was followed appropriately, 78% of initial serum concentrations and 66% of repeat serum concentrations were within the therapeutic range of 10 to 20 mg/L. Several authors have also demonstrated that the 'condition correction factor' method for estimating theophylline clearance is of limited value. The individualised methods of Chiou, Koup and Vozeh have been evaluated in over 300 patients. In addition, numerous authors have reported the relative predictive performance of Bayesian dosing programs for theophylline. All methods continue to be a rapid and accurate means of individualizing dosing requirements for patients with a diverse range of theophylline disposition characteristics. Overall, the Bayesian predictions have been less biased and slightly more precise than the pharmacokinetics-based dosing methods. The most recent cost-effectiveness data has shown that a pharmacokinetic dosing program resulted in fewer toxic serum concentrations (18.9% vs 37.8%), a shorter mean duration of hospital stay (6.3 vs 8.7 days) and more therapeutic concentrations with subsequent oral therapy (71.1% vs 44.4%) than among control patients receiving dosages prescribed by physicians.

Algorithms↗
PubMed1997

Concerted evolution at a multicopy locus in the protozoan parasite Theileria parva: extreme divergence of potential protein-coding sequences.

Concerted evolution of multicopy gene families in vertebrates is recognized as an important force in the generation of biological novelty but has not been documented for the multicopy genes of protozoa. A multicopy locus, Tpr, which consists of tandemly arrayed open reading frames (ORFs) containing several repeated elements has been described for Theileria parva. Herein we show that probes derived from the 5'/N-terminal ends of ORFs in the genomic DNAs of T. parva Uganda (1,108 codons) and Boleni (699 codons) hybridized with multicopy sequences in homologous DNA but did not detect similar sequences in the DNA of 14 heterologous T. parva stocks and clones. The probe sequences were, however, protein coding according to predictive algorithms and codon usage. The 3'/C-terminal ends of the Uganda and Boleni ORFs exhibited 75% similarity and identity, respectively, to the previously identified Tpr1 and Tpr2 repetitive elements of T. parva Muguga. Tpr1-homologous sequences were detected in two additional species of Theileria. Eight different Tpr1-homologous transcripts were present in piroplasm mRNA from a single T. parva Muguga-infected animal. The Tpr1 and Tpr2 amino acid sequences contained six predicted membrane-associated segments. The ratio of synonymous to nonsynonymous substitutions indicates that Tpr1 evolves like protein-encoding DNA. The previously determined nucleotide sequence of the gene encoding the p67 antigen is completely identical in T. parva Muguga, Boleni, and Uganda, including the third base in codons. The data suggest that concerted evolution can lead to the radical divergence of coding sequences and that this can be a mechanism for the generation of novel genes.

Amino Acid Sequence↗
PubMed1989

Kinetics of tryptic hydrolysis as a probe of the structure of human plasma apolipoprotein A-II.

As a model system to understand apolipoprotein structure-function and their relationships to proteolytic events, the kinetics of tryptic hydrolysis of apolipoprotein A-II (apo A-II) was investigated in solution and in association with phospholipid. The rates of appearance and identities of specific peptides were determined by reversed-phase high-performance liquid chromatography and amino acid analysis, respectively. For the kinetics of hydrolysis of apo A-II in solution, the carboxyl-terminal peptides of residues 55-77 and 56-77 appeared first, followed by peptides of residues 4-23, 29-39, 40-44 and 45-54, which appeared at nearly identical rates. The kinetics of hydrolysis of apo A-II associated with 1,2-dimyristoyl-sn-glycero-3-phosphocholine showed several differences. First, a 100-fold larger amount of trypsin was needed to obtain a similar rate of product formation; second, a new peptide appeared, eluting earlier than apo A-II but having a similar amino acid composition; and third, the relative rates of appearance of peptides were different. The secondary structure surrounding the bonds susceptible to trypsin cleavage was determined by several predictive algorithms. The lysine amino acid bonds were found to be in regions defined by a high helical amphipathic moment. The reduced susceptibility to tryptic hydrolysis of apo-II associated with phospholipid appears to be due to a higher free energy of stabilization of protein secondary structure. As a consequence, the lysine amino acid bonds are in folded regions of the protein where they are conformationally inaccessible to enzymatic hydrolysis. By use of structure-prediction methods, it is possible to designate which regions of apolipoproteins may be important in proteolysis.

Amino Acid Sequence↗
PubMed2002

Prediction of the need for red cell transfusion in newly diagnosed ovarian cancer patients undergoing platinum-based treatment.

OBJECTIVE: The objective of this study was to develop a predictive algorithm for the likelihood of red blood cell transfusion in women with ovarian cancer undergoing platinum-based chemotherapy. METHODS: Patients in this analysis came from two phase III studies conducted by the Southwest Oncology Group and Gynecologic Oncology Group of platinum-based chemotherapy in advanced ovarian cancer patients, SWOG 8412 and SWOG 8501/GOG 104. The probability of packed red blood cell (PRBC) transfusion was modeled as a function of stage of disease, age, weight, creatinine clearance, hemoglobin (Hb) prior to the start of therapy, the platinum agent administered (i.e., cisplatin vs carboplatin), and the route of drug administration (i.e., intravenous vs intraperitoneal). RESULTS: Overall, 16% of patients developed at least grade 3 anemia (Hb < 8 g/dL) during primary chemotherapy, with 2% experiencing grade 4 anemia (Hb < 6.5 g/dL). PRBC transfusions were administered to 32% of patients. Factors that were determined to be predictive of PRBC transfusions were age and baseline Hb. In patients with bulky stage III or stage IV disease, the odds of transfusion increased by 66% for each 10-year increase in age and by 65% for each 1 g/dL decrease in baseline hemoglobin. Thus a patient aged 65 with a baseline Hb of 10.5 g/dL has approximately a 40% chance of transfusion. CONCLUSIONS: Older ovarian cancer patients (>65 years) with low baseline Hb levels (<10.5) at initiation of platinum-based chemotherapy are likely to become more anemic during treatment and should be considered for prophylactic erythropoietin therapy as an alternative to transfusion.

Aged↗
PubMed1983

Secondary structure of bovine beta-lactoglobulin B.

Secondary-structure-prediction algorithms have been used to find the segments of beta-lactoglobulin sequence most likely to fit the circular dichroism assignment of 15% alpha-helix, 50% beta-sheet, and 15-20% reverse turn. A number of segments may have an alpha-helical conformation but the most prominent region of alpha-helix is from residue 129 to 143. A further probable alpha-helix segment is residues 65-76. The number of residues predicted to occur in segments of beta-sheet structure is less than expected. However, the most likely segments are for residues 1-6, 11-16, 39-45, 80-85, 92-96, 101-107, 117-123, and 145-151. Predicted reverse-turn tetrapeptides are residues 7-10, 49-52, 61-64, 88-91, and 112-115. These predicted secondary structures are consistent with the low-resolution structure of the molecule determined by X-ray diffraction studies.

Amino Acid Sequence↗
PubMed1994

A pharmacodynamic approach to the estimate of carbamazepine autoinduction.

Population-based pharmacokinetic prediction algorithms have been developed for several medications. A fundamental assumption has been that the kinetics remain constant over time. Carbamazepine (CBZ), however, induces its own metabolism in a concentration- and time-dependent manner. A Bayesian estimation program is presented that models the changing catabolic enzyme activity, linearly related to hepatic microsomal enzyme concentration, along with the serum drug concentration. An Emax model is used for enzyme formation with respect to drug concentration: elimination of enzyme activity is modeled as a first-order process. This program was tested in 22 drug-naive outpatients begun on CBZ monotherapy. The 1 week concentrations were used to prospectively predict concentrations at 1 month of therapy and were very close to actual measurements: prediction bias (mean error of prediction) = -0.1 micrograms/mL and precision (median absolute error of prediction) = 1.2 micrograms/mL. Comparison estimates, made by assuming a constant concentration/dose ratio, had bias = 2.6 micrograms/mL (p < 0.001) and precision = 2.2 micrograms/mL (p = 0.01). We conclude that (1) CBZ autoinduction is not complete after 1 week of therapy and (2) the methodology permits accurate estimation of CBZ pharmacokinetics.

Adult↗
PubMed2004

'Frankenstein genes', or the Mad Magazine version of the human pseudogenome.

Annotation of the human genome is inching forward. Seven human chromosomes have now been fully annotated, covering 17 per cent of the genome, and at least one chromosome has been re-annotated. The enormity of the task forces a dependence on automated tools for detecting and assembling the genes, followed by hand curation to correct errors and polish the gene models. The accuracy of gene prediction algorithms is very good for internal exons from intact genes, but these programs do peculiar and exasperating things to pseudogenes. These programs can actually resurrect pseudogenes from the dead, making them into viable gene models for intact proteins, albeit science-fictional proteins. This process is demonstrated for four human pseudogenes from the cytochrome P450 family and one putatively functional P450 gene, CYP2U1, having a non-consensus intron boundary. These examples are offered as a call-to-arms to improve pseudogene prediction as an art in itself, and not as a by-product of gene annotation. Failure to do so will flood the databases with thousands of false-positive predictions. Indeed, they are already there.

Amino Acid Sequence↗
PubMed2001

Rational selection and quantitative evaluation of antisense oligonucleotides.

Antisense oligonucleotides are an attractive therapeutic option to modulate specific gene expression. However, not all antisense oligonucleotides are effective in inhibiting gene expression, and currently very few methods exist for selecting the few effective ones from all candidate oligonucleotides. The lack of quantitative methods to rapidly assess the efficacy of antisense oligonucleotides also contributes to the difficulty of discovering potent and specific antisense oligonucleotides. We have previously reported the development of a prediction algorithm for identifying high affinity antisense oligonucleotides based on mRNA-oligonucleotide hybridization. In this study, we report the antisense activity of these rationally selected oligonucleotides against three model target mRNAs (human lactate dehydrogenase A and B and rat gp130) in cell culture. The effectiveness of oligonucleotides was evaluated by a kinetic PCR technique, which allows quantitative evaluation of mRNA levels and thus provides a measure of antisense-mediated decreases in target mRNA, as occurs through RNase H recruitment. Antisense oligonucleotides that were predicted to have high affinity for their target proved effective in almost all cases, including tests against three different targets in two cell types with phosphodiester and phosphorothioate oligonucleotide chemistries. This approach may aid the development of antisense oligonucleotides for a variety of applications.

Animals↗
PubMed2004

Filling gaps in a metabolic network using expression information.

MOTIVATION: The metabolic models of both newly sequenced and well-studied organisms contain reactions for which the enzymes have not been identified yet. We present a computational approach for identifying genes encoding such missing metabolic enzymes in a partially reconstructed metabolic network. RESULTS: The metabolic expression placement (MEP) method relies on the coexpression properties of the metabolic network and is complementary to the sequence homology and genome context methods that are currently being used to identify missing metabolic genes. The MEP algorithm predicts over 20% of all known Saccharomyces cerevisiae metabolic enzyme-encoding genes within the top 50 out of 5594 candidates for their enzymatic function, and 70% of metabolic genes whose expression level has been significantly perturbed across the conditions of the expression dataset used. AVAILABILITY: Freely available (in Supplementary information).

Algorithms↗