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PubMed1993

Symmetry and secondary structure of the replication terminator protein of Bacillus subtilis: sedimentation equilibrium and circular dichroic, infrared, and NMR spectroscopic studies.

We have used analytical ultracentrifugation in combination with a number of spectroscopic techniques to analyze the symmetry and secondary structure of the DNA-binding replication terminator protein (RTP) of Bacillus subtilis. Sedimentation equilibrium studies confirm that RTP is a dimer in solution under the conditions used for spectroscopic analysis, whereas the number of cross peaks displayed in 1H-15N HSQC NMR spectra of uniformly 15N-labeled RTP are consistent with the primary structure of the monomer. These two results in combination lead to the conclusion that RTP is a symmetric dimer in solution. Circular dichroic and Fourier-transform infrared spectra reveal, in contrast to the results obtained from a number of commonly used secondary structure prediction algorithms, that RTP contains 20-30% alpha-helical and 40-50% beta-sheet/beta-turn secondary structure and that the conformation of the protein remains unchanged over the pH range 5-8. It is proposed on the basis of protein folding-class prediction algorithms, in combination with various physical properties of RTP, that it belongs to the alpha + beta protein-folding class.

Algorithms↗
PubMed2004

Fractional scan algorithms for low-dose perfusion CT.

One of the key considerations in CT perfusion is the X-ray dose received by the patient, since cine acquisition mode is typically used in which repeated x-ray exposure occurs at the same anatomical location. In this technical note, we propose a new approach for dose reduction in which the X-ray tube current is maintained and the number of projection views is reduced per gantry rotation. A projection interpolation algorithm and an image prediction algorithm are developed to address the incompleteness of such projection data. Both algorithms utilize a priori knowledge that the contrast-uptake in perfusion images is gradual and predictable. As a result, excellent perfusion images can be reconstructed at a fraction of the nominal radiation dose.

Algorithms↗
PubMed2006

Towards robotized beating heart TECABG: assessment of the heart dynamics using high-speed vision.

Active robotic filtering is probably the solution for beating heart Totally Endoscopic Coronary Artery Bypass Grafting (TECABG). In this work, we assess the heart motion dynamics by simultaneous use of high-speed imaging of optical markers attached to the heart, ECG signals and ventilator airflow acquisitions. Our goal is to assess the heart motions (shape, velocity, acceleration) in order to be able to make more accurate specifications for a novel, dedicated robot that could follow these motions in real time. Furthermore, using two additional inputs (ECG and airflow), we propose a novel robust prediction algorithm that could be used with a predictive control algorithm to improve the tracking accuracy.

Algorithms↗
PubMed2004

A prediction model for superimposed preeclampsia in women with chronic hypertension during pregnancy.

OBJECTIVE: Women with chronic hypertension are at increased risk for superimposed preeclampsia. We developed a prediction algorithm for superimposed preeclampsia using clinical and laboratory information that were measured early in pregnancy. STUDY DESIGN: A secondary analysis of data that were collected from 110 women with chronic hypertension who were enrolled in a trial of calcium supplementation was performed. Blood pressure, the renin-angiotensin system, and calcium metabolism were assessed at 12, 20, 28, and 36 weeks of gestation and 6 weeks after delivery. Multivariable logistic regression was used to develop the predictive model. RESULTS: Thirty-seven women had superimposed preeclampsia. The final model included systolic blood pressure, serum uric acid, and plasma renin activity, which were all measured at 20 weeks of gestation. Women with high systolic blood pressure (>140 mm Hg), elevated uric acid (>3.6 mg/dL), and low plasma renin activity (<4 ng/mL/hr) had an 86% probability of having superimposed preeclampsia. Women with 2 risk factors had a 62% probability of superimposed preeclampsia, and women with only 1 risk factor had a 30% to 40% probability of superimposed preeclampsia. CONCLUSION: We developed a prediction algorithm that can be validated in future studies for superimposed preeclampsia for women with chronic hypertension.

Adult↗
PubMed1980

Fast algorithm for predicting the secondary structure of single-stranded RNA.

A computer method is presented for finding the most stable secondary structures in long single-stranded RNAs. It is 1-2 orders of magnitude faster than existing codes. The time required for its application increases as N3 for a chain N nucleotides long. As many as 1000 nucleotides can be searched in a single run. The approach is systematic and builds an optimal structure in a straightforward inductive procedure based on an exact mathematical algorithm. Two simple half-matrices are constructed and the best folded form is read directly from the second matrix by a simple back-tracking procedure. The program utilizes published values for base-pairing energies to compute one structure with the lowest free energy.

Base Sequence↗
PubMed2006

Rnall: an efficient algorithm for predicting RNA local secondary structural landscape in genomes.

BACKGROUND: The information of RNA local secondary structures (LSSs) can help retrieve biologically important motifs and study functions of RNA molecules. Most of the current RNA secondary structure prediction tools are not suitable for RNA LSS prediction on the genome scale due to high computational complexity. METHODS: We developed a new computer package Rnall based on a dynamic programming technique, which scans an RNA sequence with a sliding window and extracts all RNA LSSs with sizes no larger than the window size using the nearest neighbor thermodynamic parameters. The worst case running time of Rnall is O(W(3)L), where W is the window size and L is the query sequence length. In practice we observed a running time of O(W(2)L). We further introduced the concept of energy landscape for illustrating RNA LSS, which may facilitate RNA motif mining on the genomic scale. RESULTS: Rnall shows better prediction accuracy than two other prediction tools Lfold and Quickfold. Rnall is also applied to scan for RNA LSSs in three genomes, and the prediction maps well with known RNA motifs. CONCLUSIONS: Rnall is designed for RNA LSS prediction and together with the energy landscape, it has unique features that could be used for RNA structural motif mining. Rnall is freely available for download at http://digbio.missouri.edu/~wanx/Rnall or http://www.sysbio.muohio.edu/Rnall.

Algorithms↗
PubMed2005

The development and utility of a clinical algorithm to predict early HIV-1 infection.

The association between self-reported clinical factors and recent HIV-1 seroconversion was evaluated in a prospective cohort of 4652 high-risk participants in the HIV Network for Prevention Trials (HIVNET) Vaccine Preparedness Study. Eighty-six individuals seroconverted, with an overall annual seroconversion rate of 1.3 per 100 person-years. Four self-reported clinical factors were significantly associated with HIV-1 seroconversion in multivariate analyses: recent history of chlamydia infection or gonorrhea, recent fever or night sweats, belief of recent HIV exposure, and recent illness lasting > or =3 days. Two scoring systems, based on the presence of either 4 or 11 clinical factors, were developed. Sensitivity ranged from 2.3% (with a positive predictive value of 12.5%) to 72.1% (with a positive predictive value of 1%). Seroconversion rates were directly associated with the number of these clinical factors. The use of scoring systems comprised of clinical factors may aid in detecting early and acute HIV-1 infection in vaccine and microbicide trials. Organizers can educate high-risk trial participants to return for testing during interim visits if they develop these clinical factors. Studying individuals during early and acute HIV-1 infection would allow scientists to investigate the impact of the intervention being studied on early transmission or pathogenesis of HIV-1 infection.

Adolescent↗
PubMedDate not supplied

[Algorithm for prediction of reconvalescent salmonellosis carriage].

Of total of 181 patients with Salmonella infection were examined by clinical and laboratory methods. As many as 124 indices characterizing biological properties of Salmonellae, a large intestine microbiocenosis status, systemic and local immunity, were investigated as well. Among these indices, the most revealing signs were defined to prognosticate the reconvalescent carrier state. Conclusion was made on the prevalence of immune mechanisms in the development of reconvalescent salmonella carriage and on the important role of the ability of a causative agent to inactivate the factors of host innate immunity in this process. Diagnostic prognosis algorithm for Salmonella bacterial carriage was worked out. Clinical testing confirmed its effectiveness.

Adolescent↗
PubMed2000

A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins.

We present a fast ab initio method for the prediction of local conformations in proteins. The program, PETRA, selects polypeptide fragments from a computer-generated database (APD) encoding all possible peptide fragments up to twelve amino acids long. Each fragment is defined by a representative set of eight straight phi/psi pairs, obtained iteratively from a trial set by calculating how fragments generated from them represent the protein databank (PDB). Ninety-six percent (96%) of length five fragments in crystal structures, with a resolution better than 1.5 A and less than 25% identity, have a conformer in the database with less than 1 A root-mean-square deviation (rmsd). In order to select segments from APD, PETRA uses a set of simple rule-based filters, thus reducing the number of potential conformations to a manageable total. This reduced set is scored and sorted using rmsd fit to the anchor regions and a knowledge-based energy function dependent on the sequence to be modelled. The best scoring fragments can then be optimized by minimization of contact potentials and rmsd fit to the core model. The quality of the prediction made by PETRA is evaluated by calculating both the differences in rmsd and backbone torsion angles between the final model and the native fragment. The average rmsd ranges from 1.4 A for three residue loops to 3.9 A for eight residue loops.

Algorithms↗
PubMed1998

Enhanced antigenicity of a four-contact-residue epitope of the measles virus hemagglutinin protein by phage display libraries: evidence of a helical structure in the putative active site.

Antigenicity and conformational propensities of synthetic peptides corresponding to the sequential epitope H236-255 of the measles virus hemagglutinin protein were investigated. This epitope corresponds to the neutralising and protective monoclonal antibody BH129 and includes Arg243, implicated in CD46-down-regulation and Arg253 that has been mapped to the putative enzymatic site. Fine mapping with truncation-, elongation-, Gly- and Ala-substitution analogues defined EL-QL as the critical residues of the minimal epitope S244ELSQL249. CD spectra of peptides, comparison with the 3D-structure of homologous sequences, and prediction algorithms suggested a helical structure with the contact residues E245L-QL249 located on the protein surface. Mimotopes obtained with a 6-mer phage display library contained a consensus Pro (important for binding) instead of Ser247 of the wild-type sequence (irrelevant for binding). The kink induced by Pro seemed to be essential to bring the 4 contact-residues in the mimotopes and in the corresponding short peptides together. CD analysis and prediction algorithms suggested that non-helical conformations of the phage insert and of the peptides may favourably mimic the antigenic helical turns of the wild-type sequence, resulting in an up to 135 times higher antigenicity of the mAb towards the mimotope peptides.

Animals↗
PubMed2006

Sequence representation and prediction of protein secondary structure for structural motifs in twilight zone proteins.

Characterizing and classifying regularities in protein structure is an important element in uncovering the mechanisms that regulate protein structure, function and evolution. Recent research concentrates on analysis of structural motifs that can be used to describe larger, fold-sized structures based on homologous primary sequences. At the same time, accuracy of secondary protein structure prediction based on multiple sequence alignment drops significantly when low homology (twilight zone) sequences are considered. To this end, this paper addresses a problem of providing an alternative sequences representation that would improve ability to distinguish secondary structures for the twilight zone sequences without using alignment. We consider a novel classification problem, in which, structural motifs, referred to as structural fragments (SFs) are defined as uniform strand, helix and coil fragments. Classification of SFs allows to design novel sequence representations, and to investigate which other factors and prediction algorithms may result in the improved discrimination. Comprehensive experimental results show that statistically significant improvement in classification accuracy can be achieved by: (1) improving sequence representations, and (2) removing possible noise on the terminal residues in the SFs. Combining these two approaches reduces the error rate on average by 15% when compared to classification using standard representation and noisy information on the terminal residues, bringing the classification accuracy to over 70%. Finally, we show that certain prediction algorithms, such as neural networks and boosted decision trees, are superior to other algorithms.

Algorithms↗
PubMedDate not supplied

The early detection research network surface-enhanced laser desorption and ionization prostate cancer detection study: A study in biomarker validation in genitourinary oncology.

Prostate-specific antigen (PSA) screening has led to a dramatic increase in prostate cancer detection with a concurrent stage migration. Although the test has revolutionized prostate cancer detection by identifying disease that is potentially curable in the majority of men, only 25% of men receiving test results of PSA > 4 ng/ml will have prostate cancer and many men receiving a normal PSA will have disease, including high-grade disease. There is a need for improved biomarkers for detecting prostate cancer. One such method of cancer detection is surface-enhanced laser desorption and ionization (SELDI). The Early Detection Research Network (EDRN) validation study for SELDI for prostate cancer is described. In a three-stage study, the portability and reproducibility of the technique will be determined; the predictive algorithm will be refined in a multi-institutional case-control population; followed by ultimate validation in the context of a prospective trial with complete disease ascertainment. The unique aspect of the EDRN SELDI validation study is the novel use of two groups of cancer cases: those cases with higher-risk disease (Gleason > or = 7) and those cases with lower-risk disease (Gleason < or = 6). This study will allow the first evaluation of a predictive algorithm that includes prognosis in disease screening. The EDRN SELDI prostate cancer biomarker validation study is a rigorous evaluation of a new detection method for prostate cancer. The methodologies used for this evaluation will prove useful for guiding future biomarker studies in this challenging disease.

Biomarkers, Tumor↗
PubMed1997

Early dose assessment following severe radiation accidents.

Early treatment of victims of high level acute whole-body x-ray or gamma exposure has been shown to improve their likelihood of survival. However, in such cases, both the magnitude of the exposure and the dosimetry profile(s) of the victim(s) are often not known in detail for days to weeks. A simple dose-prediction algorithm based on lymphocyte kinetics as documented in prior radiation accidents is presented here. This algorithm provides an estimate of dose within the first 8 h following an acute whole-body exposure. Early lymphocyte depletion kinetics after a severe radiation accident follow a single exponential, L(t) = L(o)e(-k(D¿t), where k(D) is a rate constant, dependent primarily on the average dose, D. Within the first 8 h post-accident, K(D) may be calculated utilizing serial lymphocyte counts. Data from the REAC/TS Radiation Accident Registry were used to develop a dose-prediction algorithm from 43 gamma exposure cases where both lymphocyte kinetics and dose reconstruction were felt to be reasonably reliable. The inverse relationship D(K) may be modeled by a simple two parameter curve of the form D = a/(1 + b/K) in the range 0 < or = D < or = 15 Gy, with fitting parameters (mean +/- SD): a = 13.6 +/- 1.7 Gy, and b = 1.0 +/- 0.20 d(-1). Dose estimated in this manner is intended to serve only as a first approximation to guide initial medical management.

Algorithms↗
PubMed2003

Signal sequence cleavage and plasma membrane targeting of the retinal rod NCKX1 and cone NCKX2 Na+/Ca2+ - K+ exchangers.

Retinal rod and cone photoreceptors express two distinct Na(+)/Ca(2+)-K(+) exchanger (NCKX) gene products. Both the rod NCKX1 and cone NCKX2 are polytopic membrane proteins thought to contain a putative cleavable signal peptide. A cleavable signal peptide is unusual for plasma membrane proteins; moreover, predictive algorithms suggest the presence of a cleavable signal peptide for all rod NCKX1 proteins and a noncleavable signal anchor for the cone NCKX2 proteins. In this study we have placed a peptide tag at different positions of the NCKX sequence to examine whether the putative signal sequence is indeed cleaved in either NCKX1 or NCKX2 proteins expressed in heterologous systems. The signal peptide was found to be, at least in part, cleaved in dolphin rod NCKX1 and in chicken and human cone NCKX2 expressed in HEK293 cells; no signal peptide cleavage was observed for chicken rod NCKX1 despite the fact that the SignalP predictive algorithm assigned this sequence to have the highest likelihood for a cleavable signal peptide among the three NCKX sequences tested here. For the two NCKX proteins that contained a cleavable signal peptide, only cleaved NCKX protein was found in the plasma membrane of HEK293 cells. Deletion of the signal sequence in both dolphin rod NCKX1 or cone NCKX2 did not affect NCKX protein synthesis but did disrupt plasma membrane targeting as judged from abolition of NCKX function and from lack of surface biotinylation. These results are consistent with delayed signal peptide cleavage for the rod and cone NCKX proteins.

Animals↗
PubMed2000

SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family.

We have developed a procedure to predict the peptide binding specificity of an SH3 domain from its sequence. The procedure utilizes information extracted from position-specific contacts derived from six SH3/peptide or SH3/protein complexes of known structure. The framework of SH3/peptide contacts defined on the structure of the complexes is used to build a residue-residue interaction database derived from ligands obtained by panning peptide libraries displayed on filamentous phage. The SH3-specific interaction database is a multidimensional array containing frequencies of position-specific contacts. As input, SH3-SPOT requires the sequence of an SH3 domain and of a query decapeptide ligand. The array, that we call the SH3-specific matrix, is then used to evaluate the probability that the peptide would bind the given SH3 domain. This procedure is fast enough to be applied to the entire protein sequence database. Panning experiments were performed to search putative specific ligands of different SH3 domains in a database of decapeptides, or in a database of protein sequences. The procedure ranked some of the natural partners of interaction of a number of SH3 domains among the best ligands of the approximately 5. 6x10(9) different decapeptides in the SWISSPROT database. We expect the predictive power of the method to increase with the enrichment of the SH3-specific matrix by interaction data derived from new complex structures or from the characterization of new ligands. The procedure was developed using the SH3 domain family as test case but its application can easily be extended to other families of protein domains (such as, SH2, MHC, EH, PDZ, etc.).

Algorithms↗
PubMedDate not supplied

[Algorithm for predicting development of HIV infection].

Described in the paper are the results of a 15-year monitoring (1986-2001) of HIV patients at the Clinic of the Institute of Immunology, Federal Department "Medbioextreme", Russia's Health Ministry. The gathered experimental data, including the immunologic, biochemical and general-clinical parameters, were comprehensively analyzed. Optimal schemes of complex HIV monitoring were designed to ensure a comparative and dynamic study of different clinical-and-laboratory indices for the purpose of defining the HIV-induced pathogenesis specificity and adequate therapeutic approaches.

Algorithms↗
PubMed1991

Haplotype specific homology scanning algorithm to predict T-cell epitopes from protein sequences.

We present a homology scanning microcomputer program to predict functional T-cell epitopes within proteins. By taking into account particular human or mouse restriction elements the predictions are made haplotype-specific. The generality of this approach is confirmed by (i) identification of well-characterized immunogenic T-cell determinants in lysozyme (ii) search for potential T epitopes on unanalysed proteins like the human beta 2-adrenoreceptor (iii) modification of non-immunogenic peptide sequences in order to generate T-cell determinants.

Algorithms↗