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PubMed1993

Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures.

The problem of protein structure prediction is formulated here as that of evaluating how well an amino acid sequence fits a hypothetical structure. The simplest and most complicated approaches, secondary structure prediction and all-atom free energy calculations, can be viewed as sequence-structure fitness problems. Here, an approach of intermediate complexity is described, which involves; (1) description of a protein structure in terms of contact interface vectors, with both intra-protein and protein-solvent contacts counted, (2) derivation of sequence preferences for 2 up to 29 contact interface types, (3) generation of numerous hypothetical model structures by placing the input sequence into a large set of known three-dimensional structures in all possible alignments, (4) evaluation of these models by summing the sequence preferences over all structural positions and (5) choice of predicted three-dimensional structure as that with the best sequence-structure fitness. Evolutionary information is incorporated by using position-dependent core weights derived from multiple sequence alignments. A number of tests of the method are performed: (1) evaluation of cyclic shifts of a sequence in its native structure; (2) alignment of a sequence in its native structure, allowing gaps; (3) alignment search with a sequence or sequence fragment in a database of structures; and (4) alignment search with a structure in a database of sequences. The main results are: (1) a native sequence can very well find its native structure among a large number of alternatives, in correct alignment; (2) substructures, such as (beta alpha)n units, can be detected in spite of very low sequence similarity; (3) remote homologous can be detected, with some dependence on the set of parameters used; (4) contact interface parameters are clearly superior to classical secondary structure parameters; (5) a simple interface description in terms of just two states, protein-protein and protein-water contacts, performs surprisingly well; (6) the use of core weights considerably improves accuracy in detection of remote homologues; (7) based on a sequence database search with a myoglobin contact profile, the C-terminal domain of a viral origin of replication binding protein is predicted to have an all-helical fold. The sequence-structure fitness concept is sufficiently general to accommodate a large variety of protein structure prediction methods, including new models of intermediate complexity currently being developed.

Amino Acid Sequence↗
PubMed1999

Forward problem solution for electrical conductivity imaging via contactless measurements.

The forward problem of a new medical imaging system is analysed in this study. This system uses magnetic excitation to induce currents inside a conductive body and measures the magnetic fields of the induced currents. The forward problem, that is determining induced currents in the conductive body and their magnetic fields, is formulated. For a general solution of the forward problem, the finite element method (FEM) is employed to evaluate the scalar potential distribution. Thus, inhomogeneity and anisotropy of conductivity is taken into account for the FEM solutions. An analytical solution for the scalar potential is derived for homogeneous conductive spherical objects in order to test FEM solutions. It is observed that the peak error in FEM solutions is less than 2%. The numerical system is used to reveal the characteristics of the measurement system via simulations. Currents are induced in a 9x9x5 cm body of conductivity 0.2 S m(-1) by circular coils driven sinusoidally. It is found that a 1 cm shift in the perturbation depth reduces the field magnitudes to approximately one-tenth. In addition, the distance between extrema increases. Further simulations carried out using different coil configurations revealed the performance of the method and provided a design perspective for a possible data acquisition system.

Diagnostic Imaging↗
PubMed2003

Modeling of adhesion in tablet compression--I. Atomic force microscopy and molecular simulation.

Adhesion problems during tablet manufacturing have been observed to be dependent on many formulation and process factors including the run time on the tablet press. Consequently, problems due to sticking may only become apparent towards the end of the development process when a prolonged run on the tablet press is attempted for the first time. It would be beneficial to predict in a relative sense if a formulation or new chemical entity has the potential for adhesion problems early in the development process. It was hypothesized that favorable intermolecular interaction between the drug molecules and the punch face is the first step or criterion in the adhesion process. Therefore, the rank order of adhesion during tablet compression should follow the rank order of these energies of interaction. The adhesion phenomenon was investigated using molecular simulations and contact mode atomic force microscopy (AFM). Three model compounds were chosen from a family of "profen" compounds. Silicon nitride AFM tips were modified by coating a 20-nm iron layer on the surfaces by sputter coating. Profen flat surfaces were made by melting and recrystallization. The modified AFM probe and each profen surface were immersed in the corresponding profen saturated water during force measurements using AFM. The work of adhesion between iron and ibuprofen, ketoprofen, and flurbiprofen in vacuum were determined to be -184.1, -2469.3, -17.3 mJ. m(-2), respectively. The rank order of the work of adhesion between iron and profen compounds decreased in the order: ketoprofen > ibuprofen > flurbiprofen. The rank order of interaction between the drug molecules and the iron superlattice as predicted by molecular simulation using Cerius(2) is in agreement with the AFM measurements. It has been demonstrated that Atomic Force Microscopy is a powerful tool in studying the adhesion phenomena between organic drug compounds and metal surface. The study has provided insight into the adhesion problems occurring during tablet compression and a direction for continued study.

Adhesiveness↗
PubMed1995

[Trends in the joint work of the National Center for Hygiene and the epidemiological hygiene inspectorates in the field of communal hygiene].

Based on cardinal problems of medical prevention, the author formulates priority lines of action for the country's health structures in the field of community health, emphasizing areas for interaction between the National Center of Hygiene and Hygiene-and-Epidemiology Inspectorates across the country. According to the author, priority problems necessitating collaborative efforts between the National Center of Hygiene and HEIs throughout the country should be focused on the following areas: updating sanitary legislation; environmental monitoring, including community and territorial planning; health risk assessment; development of an efficient health-information system concerning environment and health; manpower training; and ecologic education of the public. Collaboration also needs to cover joint implementation of projects at international collaboration level along the lines of the World Health Organization, the PHARE programs, etc. The priorities referred to also reflect the conception of medical prevention functions in the area of community health.

Bulgaria↗
PubMed1999

Changing cyclosporin A formulation: an analysis in paediatric cardiac transplant recipients.

Cyclosporin A is the primary immunosuppressive agent used in cardiac transplantation to maintain chronic immunosuppression. Absorption may be erratic and major side-effects include nephrotoxicity. A recently introduced formulation (Neoral) improves absorption in cystic fibrosis heart-lung transplant recipients, but episodes of rejection have been reported on conversion from the oil-based formulation. A retrospective analysis of 21 paediatric cardiac transplant recipients who had been converted from the oil-based formulation to the micro-emulsified formulation was performed. No clinical rejection episodes occurred following conversion. There was a significant reduction in dose following conversion (p < 0.001). The mean trough level was less on the new formulation (p = 0.04), but there was no difference in coefficient of variation or standard deviation. Mean glomerular filtration rate (GFR) was significantly less, but there was no difference in the rate of change of GFR on the new formulation. Erratic absorption and deteriorating renal function remain as significant problems in paediatric cardiac transplant recipients despite conversion to the new formulation.

Adolescent↗
PubMed2006

The multiple common point set problem and its application to molecule binding pattern detection.

Recognition of binding patterns common to a set of protein structures is important for recognition of function, prediction of binding, and drug design. We consider protein binding sites represented by a set of 3D points with assigned physico-chemical and geometrical properties important for protein-ligand interactions. We formulate the multiple binding site alignment problem as detection of the largest common set of such 3D points. We discuss the computational problem of multiple common point set detection and, particularly, the matching problem in K-partite-epsilon graphs, where K partitions are associated with K structures and edges are defined between epsilon-close points. We show that the K-partite-epsilon matching problem is NP-hard in the Euclidean space with dimension larger than one. Consequently, we show that the largest common point set problem between three point sets is NP-hard. On the practical side, we present a novel computational method, MultiBind, for recognition of binding patterns common to a set of protein structures. It performs a multiple alignment between protein binding sites in the absence of overall sequence, fold, or binding partner similarity. Despite the NP-hardness results, in our applications, we practically overcome the exponential number of multiple alignment combinations by applying an efficient branchand- bound filtering procedure. We show applications of MultiBind to several biological targets. The method recognizes patterns which are responsible for binding small molecules, such as estradiol, ATP/ANP, and transition state analogues.

Adenosine Triphosphate↗
PubMed1996

Design of adiabatic selective pulses using optimal control theory.

Optimal control theory has been applied in the past for the design of RF pulses for selective excitation. This was the outcome of having established the controllability of the MR spin system for the selective excitation problem. "Minimum distance" was the main formulation used for the solution. Because of their robust behavior in the presence of inhomogeneous RF fields, adiabatic pulses play an important role in spin inversion and excitation. In this study, we present a method for incorporating adiabaticity into the optimal control problem by enhancing the cost functional with an appropriate term. Two different types of adiabatic terms are proposed. Furthermore, two methods are used to solve the optimal control problem, namely the Hamiltonian approach and the solution by mathematical programming. Design examples include both a frequency selective pulse for performing fat suppression by inversion and a regular inversion pulse. It is shown that, in the course of optimization, the pulse designer can trade-off slice resolution against pulse adiabaticity.

Humans↗
PubMed2004

Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach.

MOTIVATION: Multiple structural alignments (MSTAs) provide position-specific information on the sequence variability allowed by protein folds. This information can be exploited to better understand the evolution of proteins and the physical chemistry of polypeptide folding. Most MSTA methods rely on a pre-computed library of pairwise alignments. This library will in general contain conflicting residue equivalences not all of which can be realized in the final MSTA. Hence to build a consistent MSTA, these methods have to select a conflict-free subset of equivalences. RESULTS: Using a dataset with 327 families from SCOP 1.63 we compare the ability of two different methods to select an optimal conflict-free subset of equivalences. One is an implementation of Reinert et al.'s integer linear programming formulation (ILP) of the maximum weight trace problem (Reinert et al., 1997, Proc. 1st Ann. Int. Conf. Comput. Mol. Biol. (RECOMB-97), ACM Press, New York). This ILP formulation is a rigorous approach but its complexity is difficult to predict. The other method is T-Coffee (Notredame et al., 2000) which uses a heuristic enhancement of the equivalence weights which allow it to use the speed and simplicity of the progressive alignment approach while still incorporating information of all alignments in each step of building the MSTA. We find that although the ILP formulation consistently selects a more optimal set of conflict-free equivalences, the differences are small and the quality of the resulting MSTAs are essentially the same for both methods. Given its speed and predictable complexity, our results show that T-Coffee is an attractive alternative for producing high-quality MSTAs.

Algorithms↗
PubMed2005

Wavelet thresholding with bayesian false discovery rate control.

The false discovery rate (FDR) procedure has become a popular method for handling multiplicity in high-dimensional data. The definition of FDR has a natural Bayesian interpretation; it is the expected proportion of null hypotheses mistakenly rejected given a measure of evidence for their truth. In this article, we propose controlling the positive FDR using a Bayesian approach where the rejection rule is based on the posterior probabilities of the null hypotheses. Correspondence between Bayesian and frequentist measures of evidence in hypothesis testing has been studied in several contexts. Here we extend the comparison to multiple testing with control of the FDR and illustrate the procedure with an application to wavelet thresholding. The problem consists of recovering signal from noisy measurements. This involves extracting wavelet coefficients that result from true signal and can be formulated as a multiple hypotheses-testing problem. We use simulated examples to compare the performance of our approach to the Benjamini and Hochberg (1995, Journal of the Royal Statistical Society, Series B57, 289-300) procedure. We also illustrate the method with nuclear magnetic resonance spectral data from human brain.

Bayes Theorem↗
PubMed2003

Transdermal administration of bromocriptine.

Bromocriptine (BRC) has been mainly used for the inhibition of lactation, treatment of menstrual disorders, Parkinson disease, breast tumours, infertility and brain tumours as a dopamine agonist in clinics. But current BRC formulations have some side effects and bioavailability problems because of hepatic first pass effect. Transdermal application could be an alternative route to overcome all these problem and penetration properties of BRC has not been studied yet. Therefore, it was aimed to investigate the effectiveness of transdermal formulation of BRC which is applicable to the skin. For this purpose, a number of BRC gel formulations (Carbopol-934 (C-934), chitosan (CH) and Gantrez-SP215 (G-SP215) were developed and the effectiveness and bioavailability of the formulations were compared in rabbits. Commercial BRC tablets (Parlodel) were also given to rabbits orally and plasma levels were compared. The effects of two different penetration enhancers, sodium taurocholate (ST) and ethoxydiglycol-Transcutol) (TR) on the BRC penetration were also investigated. The skin samples from the dorsal part of the rabbit were removed after CH gel application and investigated under electron microscope to understand the effects of the gel on the penetration and the possible penetration mechanisms through skin were also discussed. In conclusion, CH gel formulation was found to be the best formulation and comparable blood BRC concentrations were obtained when applied to the rabbit skin. Higher blood levels were obtained with the use of CH. The main penetration process was found to be through transcellular route but some other mechanisms were also found to be incorporated, after microscopic investigation. CH gel was found to be a useful carrier for BRC administration through dermal route and the penetration enhancing effect and the mechanism of CH gel were first established in this study. It was concluded that transdermal delivery of BRC may be a very promising alternative route to the oral route for the treatment.

Administration, Cutaneous↗
PubMed1986

Analog "neuronal" networks in early vision.

Many problems in early vision can be formulated in terms of minimizing a cost function. Examples are shape from shading, edge detection, motion analysis, structure from motion, and surface interpolation. As shown by Poggio and Koch [Poggio, T. & Koch, C. (1985) Proc. R. Soc. London, Ser. B 226, 303-323], quadratic variational problems, an important subset of early vision tasks, can be "solved" by linear, analog electrical, or chemical networks. However, in the presence of discontinuities, the cost function is nonquadratic, raising the question of designing efficient algorithms for computing the optimal solution. Recently, Hopfield and Tank [Hopfield, J. J. & Tank, D. W. (1985) Biol. Cybern. 52, 141-152] have shown that networks of nonlinear analog "neurons" can be effective in computing the solution of optimization problems. We show how these networks can be generalized to solve the nonconvex energy functionals of early vision. We illustrate this approach by implementing a specific analog network, solving the problem of reconstructing a smooth surface from sparse data while preserving its discontinuities. These results suggest a novel computational strategy for solving early vision problems in both biological and real-time artificial vision systems.

Humans↗
PubMed2002

Validation of a HPLC quantification of acetaminophen, phenylephrine and chlorpheniramine in pharmaceutical formulations: capsules and sachets.

Acetaminophen, phenylephrine and chlorpheniramine are frequently associated in pharmaceutical formulations against the common cold. Their quantification presents several problems. A HPLC method for the simultaneous determination of these compounds in pharmaceutical formulations such as capsules and sachets, including the separation of impurities and excipients has been developed and validated. The selectivity of the method was also tested to be used if phenylpropanolamine hydrochloride were employed instead of phenylephrine. Final chromatographic conditions were a gradient elution, being solvent A: phosphate buffer 40 mM at pH 6.0 and solvent B: acetonitrile. At t=0, the mobile phase consisted of 92% A and 8% B and it changed with a linear gradient during 8 min to 75% A and 25% B. At min 8, it changed to 30% A and 70% B for 5 min and at t=15 min, it returns to the initial conditions (92% A and 8% B) during 1 min remaining at this composition until t=20 min. UV detection was performed at 215 nm for phenylephrine and chlorpheniramine, because at this wavelength sensitivity was higher than in other more characteristic wavelengths and it was necessary for the detection of minor compounds. For acetaminophen 280 nm was employed. Validation parameters permit to consider the method adequate.

Acetaminophen↗
PubMedDate not supplied

The development of formocresol as a medicament for primary molar pulpotomy procedures.

The development of formocresol as a pulpotomy medicament is charted from the 19th Century to the present day. While the solution has come in and out of vogue, few agents can seriously challenge its efficacy. Doubts about its toxicity, mutagenicity, and carcinogenicity have led, however, to a call for a more dilute formulation as well as a review of alternative medicaments. Problems arise in deriving an appropriate formula for a dilute version from existing formulations, which appear to have misinterpreted the concentration of constituents in the original solution.

Europe↗
PubMed1992

Using fragment lengths from incomplete digestion by multiply cleaving enzymes to map antibody binding sites on a protein.

The problem of mapping the positions of the unique binding sites of several monoclonal antibodies on a linear protein structure is considered. Data giving the incidence of binding of individual antibodies to fragments of the protein obtained from it by the incomplete chemical or enzymatic digestion are used to formulate a series of linear programming problems. The solution to these problems shows which orderings of binding sites are possible, and gives upper and lower bounds for the relative positions of the sites.

Algorithms↗
PubMed1990

The status and use of the International Classification of Impairments, Disabilities and Handicaps (ICIDH).

International monitoring of the ICIDH has begun in earnest. The momentum from these new activities and organizations has worked towards the unification and harmonization of statistics and information devoted to the study of disablement, further enhancing the interdisciplinary nature of the study of disability and advancing its recognition both at the national and international level. This article introduces the reader to the definitions and concepts of the ICIDH. In addition, problems confronted when applying the ICIDH in policy formulation, programme implementation and evaluation and in research are reviewed. There are three main types of problem: (i) the difficulty in differentiating each of the concepts of impairment, disability and handicap at the operational level of human function and behaviour; (ii) the diversity of training and instructions required in order to orchestrate the use of the codes and classification schemes with persons having a wide range of expertise and analytical interests; and (iii) the need for consistency of use of the ICIDH for model-building and testing of different theoretical frameworks. Increased institutional development at the global level through the establishment of international networks, and regional and interregional programmes, have further clarified strengths and weaknesses of the ICIDH and have increased support of its use. These efforts suggest the increasing importance of the ICIDH for the future development of international statistical standards and recommendations in the field of disablement.

Activities of Daily Living↗
PubMed2003

Pharmacokinetic comparison of fast-disintegrating and conventional tablet formulations of risperidone in healthy volunteers.

BACKGROUND: Difficulties with and resistance to tablet-taking are common in all patient groups and can exacerbate compliance problems and undermine treatment efficacy. In recent years, rapidly dissolving oral drug formulations have been developed to overcome problems related to swallowing difficulties. OBJECTIVE: The goal of this study was to evaluate the bioequivalence of a fast-disintegrating oral tablet of risperidone and the conventional oral tablet. METHODS: This was a randomized, open-label, 2-way crossover trial in which healthy volunteers received two 0.5-mg tablets of a fast-disintegrating oral risperidone formulation and two 0.5-mg tablets of conventional oral risperidone, each in a single administration. Blood samples for pharmacokinetic analysis of the active moiety (risperidone + 9-hydroxy-risperidone), risperidone, and its active metabolite 9-hydroxy-risperidone were obtained during a 96-hour period after dosing. Safety assessments included monitoring of adverse events, hematology and biochemistry tests of the sampled blood, urinalysis, blood pressure measurements, and electrocardiography. RESULTS: The bioequivalence assessment was based on pharmacokinetic and statistical analysis of data from 37 subjects who completed both treatment periods. The plasma concentration-time profiles of the active moiety, risperidone, and 9-hydroxy-risperidone were similar after intake of the 2 formulations. The fast-disintegrating tablet and the conventional tablet showed bioequivalence with respect to the active moiety, risperidone, and 9-hydroxy-risperidone. The 90% CIs for the mean treatment ratios of the log-transformed peak plasma concentration, area under the plasma concentration-time curve (AUC) to the last quantifiable time point, and AUC extrapolated to infinity were all within the predefined equivalence range from 80% to 125%. Twenty-eight of 50 (56%) subjects originally randomized reported adverse events, with a similar incidence for both treatments. All adverse events were mild, with somnolence and headache being the most frequently reported. No clinically relevant changes were observed in physical, biochemical, hematologic, or urinalysis variables during the study. CONCLUSION: In this study in healthy subjects, a single administration of two 0.5-mg fast-disintegrating risperidone tablets was bioequivalent to a single administration of two 0.5-mg conventional risperidone tablets.

Adult↗
PubMed1997

Optimisation algorithms for ECG data compression.

The use of exact optimisation algorithms for compressing digital electrocardiograms (ECGs) is demonstrated. As opposed to traditional time-domain methods, which use heuristics to select a small subset of representative signal samples, the problem of selecting the subset is formulated in rigorous mathematical terms. This approach makes it possible to derive algorithms guaranteeing the smallest possible reconstruction error when a bounded selection of signal samples is interpolated. The proposed model resembles well-known network models and is solved by a cubic dynamic programming algorithm. When applied to standard test problems, the algorithm produces a compressed representation for which the distortion is about one-half of that obtained by traditional time-domain compression techniques at reasonable compression ratios. This illustrates that, in terms of the accuracy of decoded signals, existing time-domain heuristics for ECG compression may be far from what is theoretically achievable. The paper is an attempt to bridge this gap.

Algorithms↗
PubMed2004

Successful multidisciplinary treatment in an adolescent case of rumination.

Rumination is a rare and complex disorder to treat. It involves repeated regurgitation, rechewing and reswallowing of food and occurs mainly among infants and mentally retarded children. Among adolescents and adults it is rather rare, but still might cause significant sequelae (depression, other eating disorders and social problems). We provide a detailed psychodynamic formulation in a non-retarded adolescent with rumination (over a four year period). A multidisciplinary approach involving individual insight-oriented psychotherapy, group therapy, pharmacological therapy and a nutritional intervention has proved successful in abating the patient's symptoms. We propose that among adolescents and adults, childhood issues of neglect and feeding problems may be reactivated through the rumination symptom. The focus of this report is to address the importance of rumination, as well as the role of a multidisciplinary approach to such cases.

Adolescent↗