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PubMed2005

Free vibrations of an electroelastic body under biasing fields.

We present a systematic analysis of the eigen-value problem associated with free, small-amplitude vibrations superposed on finite biasing fields in an electroelastic body. An abstract formulation is introduced. The operators in the abstract formulation are shown to be self-adjoint, from which a series of fundamental properties of resonant frequencies and modes are proved concisely. A variational formulation and a perturbation analysis of the eigenvalue problem also are given based on the abstract formulation.

Journal Article↗

PubMed1997

Sexual satisfaction and dysfunction in marriages of male alcoholics: comparison with nonalcoholic maritally conflicted and nonconflicted couples.

OBJECTIVE: This study examined the contribution of alcoholism and marital conflict to male alcoholics' sexual problems. METHOD: Married couples with an alcoholic husband (n = 26) were compared with 26 maritally conflicted and 26 nonconflicted couples without alcohol-related problems on both sexual dysfunction and sexual satisfaction. RESULTS: The male alcoholics and their wives experienced less sexual satisfaction across a range of variables and more sexual dysfunction-specifically husbands' diminished sexual interest, impotence and premature ejaculation, and wives' painful intercourse-than nonconflicted couples. However, impotence was the only aspect on which alcoholics reported more difficulties than did maritally conflicted couples. When husbands' age was considered, more frequent retarded ejaculation with older age was unique to the alcoholics since it did not occur in conflicted or nonconflicted husbands; and there was a greater decline in frequency of intercourse with older age among the alcoholic than among the conflicted couples. CONCLUSIONS: These findings are consistent with a biopsychosocial formulation of alcoholics' sexual adjustment problems that implicates (1) marital conflict as a major contributing factor to most of these problems and (2) the combined role of both marital conflict and the physical effects of chronic alcohol abuse as most relevant to the elevated rates of impotence and retarded ejaculation (among older alcoholics) and the steeper decline in intercourse frequency with age.

Adult↗

PubMed2005

Platelet cryopreservation using a trehalose and phosphate formulation.

Long-term storage of platelets is infeasible due to platelet activation at low temperatures. In an effort to address this problem, we evaluated the effectiveness of a formulation combining trehalose and phosphate in protecting platelet structure and function following cryopreservation. An annexin V binding assay was used to quantify the efficacy of the trehalose and phosphate formulation in suppressing platelet activation during cryopreservation. Of the platelets cryopreserved with the trehalose plus phosphate formulation, 23% +/- 1.2% were nonactivated, compared with 9.8% +/- 0.26% nonactivated following cryopreservation with only trehalose. The presence of both trehalose and phosphate in the cryopreservation medium is critical for cell survival and preincubation in trehalose plus phosphate solutions further enhances viability. The effectiveness of trehalose plus phosphate in preserving platelets in a nonactivated state is comparable to 6% dimethyl sulfoxide (Me(2)SO). Measurements of platelet metabolic activity using an alamarBlue assay also established that trehalose plus phosphate is superior to trehalose alone. Finally, platelets protected by the trehalose plus phosphate formulation exhibit similar aggregation response upon thrombin addition as fresh platelets, but an increase of cytosolic calcium concentration upon thrombin addition was not observed in the cryopreserved platelets. These results suggest that trehalose and phosphate protect several aspects of platelet structure and function during cryopreservation, including an intact plasma membrane, metabolic activity, and aggregation in response to thrombin, but not intracellular calcium release in response to thrombin.

Annexin A5↗

PubMed2005

A finite-element model of the aperture method for determining the effective radiating area of physiotherapy treatment heads.

This paper describes a theoretical study of the way in which a circular aperture placed in front of a plane-piston modifies the ultrasonic field it generates. Specifically, the radiated acoustic power transmitted by the aperture and the radiation force experienced by an absorbing target placed in the transmitted beam, are evaluated at a distance from the exit-side of the aperture. The calculations used a finite element (FE) method, in conjunction with a surface Helmholtz integral formulation to solve the fluid/structure interaction problem. The PAFEC (Program for Automatic Finite Element Computation) vibroacoustics software was used for the FE calculations and the implementation of the surface Helmholtz integral formulation method. Acoustic pressures and particle velocities were computed at required points, whilst accounting for the presence of the aperture in the medium, together with its dynamic properties when subjected to an incident sound field. This enabled the calculation of the radiation force on the absorber and its variation with the applied aperture diameter was investigated. As part of the validation process for the new FE aperture model, the ratio of radiation force to radiated acoustic power obtained using the FE method in the unapertured case, through the use of the Rayleigh integral, yielded good agreement with results obtained through an analytical solution. The study has been carried out to provide a better understanding of the factors affecting the measurement uncertainty for the aperture method of determining the effective radiating area (A(ER)) of physiotherapy ultrasound treatment heads.

Acoustics↗

PubMed2006

Directed percolation with incubation times.

We introduce a model for directed percolation with a long-range temporal diffusion, while the spatial diffusion is kept short ranged. In an interpretation of directed percolation as an epidemic process, this non-Markovian modification can be understood as incubation times, which are distributed accordingly to a Lévy distribution. We argue that the best approach to find the effective action for this problem is through a generalization of the Cardy-Sugar method, adding the non-Markovian features into the geometrical properties of the lattice. We formulate a field theory for this problem and renormalize it up to one loop in a perturbative expansion. We solve the various technical difficulties that the integrations possess by means of an asymptotic analysis of the divergences. We show the absence of field renormalization at one-loop order, and we argue that this would be the case to all orders in perturbation theory. Consequently, in addition to the characteristic scaling relations of directed percolation, we find a scaling relation valid for the critical exponents of this theory. In this universality class, the critical exponents vary continuously with the Lévy parameter.

Journal Article↗

PubMed1991

Parental adaptation to adolescent drug abuse: an ethnographic study of role formulation in response to courtesy stigma.

Community based nurses have increasingly been involved in caring for the parents of drug abusing adolescents. They are in need of research data about how parents are coping with the problem. This study analyzed parental role formulation in response to their position as parents of deviant children. The method of inquiry was ethnographic. Data were gathered from nonparticipant observations, parent informant journals, and interviews with parents involved in a survival group. Parents move through three phases of role formation, the content of which has implications for nursing assessments. The similarities of these parents to those of physically and mentally handicapped children is striking. Both are outside the conventional norm and are constantly involved in interpreting situations with others as to their different parenting role. A pecularity in the findings is that the parents were less discredited by their family and friends than had been anticipated. They met their greatest discreditation from community institutions, including the school, police, and court systems, institutions that were expected to assist them in bringing their child's drug abuse under control.

Adolescent↗

PubMed2006

MotifCut: regulatory motifs finding with maximum density subgraphs.

MOTIVATION: DNA motif finding is one of the core problems in computational biology, for which several probabilistic and discrete approaches have been developed. Most existing methods formulate motif finding as an intractable optimization problem and rely either on expectation maximization (EM) or on local heuristic searches. Another challenge is the choice of motif model: simpler models such as the position-specific scoring matrix (PSSM) impose biologically unrealistic assumptions such as independence of the motif positions, while more involved models are harder to parametrize and learn. RESULTS: We present MotifCut, a graph-theoretic approach to motif finding leading to a convex optimization problem with a polynomial time solution. We build a graph where the vertices represent all k-mers in the input sequences, and edges represent pairwise k-mer similarity. In this graph, we search for a motif as the maximum density subgraph, which is a set of k-mers that exhibit a large number of pairwise similarities. Our formulation does not make strong assumptions regarding the structure of the motif and in practice both motifs that fit well the PSSM model, and those that exhibit strong dependencies between position pairs are found as dense subgraphs. We benchmark MotifCut on both synthetic and real yeast motifs, and find that it compares favorably to existing popular methods. The ability of MotifCut to detect motifs appears to scale well with increasing input size. Moreover, the motifs we discover are different from those discovered by the other methods. AVAILABILITY: MotifCut server and other materials can be found at motifcut.stanford.edu.

Algorithms↗

PubMed1979

The inability to transfer classroom learning to clinical nursing practice: a learning problem and its remedial plan.

The inability to transfer classroom knowledge to clinical nursing practice is a common learning problem encountered by many nursing students. Manifestations of this problem may involve both the academic performance and personal development of the students: inability to solve problems in nursing situations; inflexibility and rigidity in the exercise of nursing care; fragmentation of nursing care; and apathy towards clinical practice. Because of the seriousness of this learning problem, a plan must be formulated to rectify it. This plan is developed with major emphasis on the teaching process, the student and the curriculum. One of the important roles of a teacher is to help students understand many widely useful relationships, principles or generalizations. In order to enhance transfer, nursing students must be given ample opportunities to apply the learned principles in a variety of nursing situations. Learning is a self-active process; an ideal transfer demands the students' conscious realization that transfer is possible. Students need to be committed to the belief that particular facts in the classroom study are pertinent in other situations. To promote transfer, the curriculum must be designed in such a way so that it has transfer value in terms of the students' goals and purposes. Furthermore, proper sequence of curricular activities is crucial if transfer of classroom knowledge to clinical practice is to occur.

Adaptation, Psychological↗

PubMed2005

A combinatorial approach to the electron correlation problem.

Starting from a path-integral formulation of quantum statistical mechanics expressed in a space of Slater determinants, we develop a method for the Monte Carlo evaluation of the energy of a correlated electronic system. The path-integral expression for the partition function is written as a contracted sum over graphs. A graph is a set of distinct connected determinants on which paths can be represented. The weight of a graph is given by the sum over exponentially large numbers of paths which visit the vertices of the graph. We show that these weights are analytically computable using combinatorial techniques, and they turn out to be sufficiently well behaved to allow stable Monte Carlo simulations in which graphs are stochastically sampled according to a Metropolis algorithm. In the present formulation, graphs of up to four vertices have been included. In a Hartree-Fock basis, this allows for paths which include up to sixfold excitations relative to the Hartree-Fock determinant. As an illustration, we have studied the dissociation curve of the N(2) molecule in a VDZ basis, which allows comparison with full configuration-interaction calculations.

Journal Article↗

PubMed1993

Systemic and local tolerability of ophthalmic drug formulations. An update.

All eye drops raise problems of local tolerance, but with variable frequencies. They can induce pain on instillation, allergic reactions, delayed healing, punctate keratitis, disturbances of lacrimal secretion, disturbances of accommodation (especially the parasympathomimetics) and local pigmentation after prolonged use. Corticosteroids are associated with 2 major risks: chronic glaucoma and cataract, initially reversible if treatment is stopped. There is still a major risk of corneal herpes with corticosteroids. It is important to be aware of these local problems as they are responsible for poor patient compliance. The systemic effects essentially concern the agonists and antagonists of the autonomic nervous system. beta-Blocker eye drops can cause bronchospasm, heart failure, syncope and psychiatric disorders, especially at high doses and with nonselective beta-blockers. These consequences are usually related to failure to comply with the prescribing precautions. alpha-Adrenergic agonists, which exert dose-dependent effects, can induce hypertensive crises or angina attacks. Apart from patients at risk (children under the age of 30 months and the elderly), parasympathomimetics cause few systemic adverse effects; anticholinesterases, which have curare-like properties, are contraindicated for 6 weeks before general anesthesia. In the very young and the very old, atropinic eye drops carry a risk of cardiovascular collapse and neuropsychiatric disturbances. Problems may also occur with other classes of drugs such as anti-infectives, antispectics, anti-inflammatories and contact lens products. Nevertheless, it is clear that this form of treatment is generally very well tolerated in relation to the volume of eye drops prescribed by ophthalmologists each day.

Adrenal Cortex Hormones↗

PubMed1989

[Endotoxemia as a problem of clinical surgery].

The authors have formulated a modern concept of endotoxicosis. The ideas of its essence were formed on the clinical model of the severe associated mechanical trauma. Principles of the complex treatment of endotoxicosis are described.

Endotoxins↗

PubMedDate not supplied

Bridges between health care research evidence and clinical practice.

Research is producing increasing amounts of important new evidence for health care, but there is a large gap between what this evidence shows can be done and the care that most patients actually receive. An important reason for this gap is the extensive processing that evidence requires before application. This article discusses a three-step model for bridging research evidence to management of clinical problems: getting the evidence straight, formulating evidence-based clinical policies, and applying evidence-based clinical policies at the right place and time. This model is purposely broad in scope and provides a framework for coordinating efforts to support evidence-based medical care. The authors' purpose is to represent the roles of health informatics in the context of the roles of all the key players, including health care researchers and practitioners, health care organizations, and the public. Health informatics has already made important contributions to bridging evidence to practice, including improving evidence retrieval, evaluation, and synthesis; new evidence-based information products; and computerized aids for facilitating the use of these products during clinical decision making. However, much more innovation and coordination are needed. The authors call for health informaticians to pay balanced attention to 1) the quality of evidence embodied in information innovations, 2) the performance of technologies and systems that retrieve, prepare, disseminate, and apply evidence, and 3) the fit of information tools to the specific clinical circumstances in which evidence is to be applied. Effective interdisciplinary teams that include health services researchers and other evidence experts, clinical practitioners, informaticians, and health care managers are needed to achieve success. Informaticians can make increasingly important contributions to the transfer of health care research by joining such teams.

Decision Making, Organizational↗

PubMedDate not supplied

[Water pipelines conduits and urban sanitation in Cartagena in the beginning of the twentieth century].

Throughout its history, Cartagena de Indias, a seaport in the Colombian Caribbean, has been handicapped for not offering salubrious conditions to its people and visitors. The lack of an aqueduct and a sewerage system was an impairment to progress. For nearly forty years (1890-1930) these problems have caused a myriad of medical discourses formulated by scientists, technicians and politicians. Cartagena's contribution to solve the sanitation problem in cities has consisted in making use of engineers' knowledge. The construction of urban facilities in the beginning of the twentieth century required a more technical knowledge, one which would advance a comprehensive solution to the water problem, ensure sufficient supply and efficient drainage. Thus, in the last turn of the century, the medical doctor is no longer the only authoritative voice when it comes to the management of urban life. The construction works which require an engineer, involving him in public health, have drawn a distinction between "hygiene" and "sanitary science".

City Planning↗

PubMed1983

A direct substitution, equation error technique for solving the thermographic tomography problem.

A new technique for solving the combined state and parameter estimation problem in thermographic tomography is presented. The technique involves the direct substitution of known skin temperatures into the finite difference form of the bio-heat transfer equation as formulated for solving an initial value problem with a convection boundary condition at the skin surface. These equations are then used to solve the inverse bio-heat transfer problem for the unknown subcutaneous tissue temperatures and physiological parameters. For a small number of nodal points, closed form algebraic solutions are obtained. For larger sets of equations, a hybrid technique is used in which the problem is initially posed as an unconstrained optimization problem in which the model equation error is minimized using the conjugate gradient descent technique to get close to a solution. Then a generalized Newton-Raphson technique was used to solve the equations. A numerical simulation of a one-dimensional problem is investigated both with and without noise superimposed on the input (transient) skin temperature data. The results show that the technique gives very accurate results if the skin temperature data contains little noise. It is also shown that if the physical properties of the tissue and the metabolism are known, that a given set of proper transient skin temperature inputs yields a unique solution for the unknown internal temperatures and blood perfusion rates. However, the similar problem with known blood perfusion rates and unknown metabolisms does not yield a unique solution for the internal temperatures and metabolisms.

Biomechanical Phenomena↗

PubMed1997

Planning controlled clinical trials. Prostatic cancer.

OBJECTIVE: To address principles in the design and conduct of clinical trials on prostate cancer (PC) with special reference to localized disease. METHODS: In advance of and during the World Health Organization (WHO) conference on Prostate Cancer in Stockholm in September 1996, 6 members of a working group evaluated and reached consensus on key points for the planning and conduction of controlled clinical trials in PC. The key points discussed were 1) hypothesis formulation, 2) general methodological principles, 3) special problems of PC trials, 4) alternatives to randomization, and 5) trial organization. RESULTS: The hypothesis must be clearly formulated and also clinically relevant enough to justify the expenses (in a broad sense) of a randomized clinical trial. Patient selection, definition of endpoints, and sample size calculations must be carefully considered and correspond to the aims of the study. Stratification on important prognostic factors should be contemplated. Maintaining the accrual rate and ensuring compliance are critical for a quality study. Survival is the main endpoint and intention to treat analysis is the standard methodology. Secondary endpoints (eg, quality of life and costs) are important for the evaluation of many treatment modalities. The use of surrogate endpoints for survival, such as prostate-specific antigen (PSA) elevation, may be misleading. Surrogate endpoints require further validation. Special features, such as long natural history in localized disease and difficulties in assessing objective responses in advanced disease, need consideration in PC trials. The controlled randomized trial is the gold standard methodology. Nonrandomized trials are often hampered by severe methodological problems, such as selection bias and biased ascertainment of endpoints due to the doctor's or patient's preferences. For the organization of a successful trial, a well-constructed study protocol is essential. Good clinical practice as defined within the European Community helps define and solve practical problems. CONCLUSIONS: The past 30 years of poorly designed clinical research on PC has left us without reliable answers in key clinical issues regarding, for example, the efficacy of primary treatment of localized PC. It is a stimulating and important challenge to the urological scientific community to conduct well-organized controlled clinical trials.

Controlled Clinical Trials as Topic↗

PubMed1996

Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods.

The predictive limits of the amino acid composition for the secondary structural content (percentage of residues in the secondary structural states helix, sheet, and coil) in proteins are assessed quantitatively. For the first time, techniques for prediction of secondary structural content are presented which rely on the amino acid composition as the only information on the query protein. In our first method, the amino acid composition of an unknown protein is represented by the best (in a least square sense) linear combination of the characteristic amino acid compositions of the three secondary structural types computed from a learning set of tertiary structures. The second technique is a generalization of the first one and takes into account also possible compositional couplings between any two sorts of amino acids. Its mathematical formulation results in an eigenvalue/eigenvector problem of the second moment matrix describing the amino acid compositional fluctuations of secondary structural types in various proteins of a learning set. Possible correlations of the principal directions of the eigenspaces with physical properties of the amino acids were also checked. For example, the first two eigenvectors of the helical eigenspace correlate with the size and hydrophobicity of the residue types respectively. As learning and test sets of tertiary structures, we utilized representative, automatically generated subsets of Protein Data Bank (PDB) consisting of non-homologous protein structures at the resolution thresholds < or = 1.8A, < or = 2.0A, < or = 2.5A, and < or = 3.0 A. We show that the consideration of compositional couplings improves prediction accuracy, albeit not dramatically. Whereas in the self-consistency test (learning with the protein to be predicted), a clear decrease of prediction accuracy with worsening resolution is observed, the jackknife test (leave the predicted protein out) yielded best results for the largest dataset (< or = 3.0A, almost no difference to the self-consistency test!), i.e., only this set, with more than 400 proteins, is sufficient for stable computation of the parameters in the prediction function of the second method. The average absolute error in predicting the fraction of helix, sheet, and coil from amino acid composition of the query protein are 13.7, 12.6, and 11.4%, respectively with r.m.s. deviations in the range of 8.6 divided by 11.8% for the 3.0 A dataset in a jackknife test. The absolute precision of the average absolute errors is in the range of 1 divided by 3% as measured for other representative subsets of the PDB. Secondary structural content prediction methods found in the literature have been clustered in accordance with their prediction accuracies. To our surprise, much more complex secondary structure prediction methods utilized for the same purpose of secondary structural content prediction achieve prediction accuracies very similar to those of the present analytic techniques, implying that all the information beyond the amino acid composition is, in fact, mainly utilized for positioning the secondary structural state in the sequence but not for determination of the overall number of residues in a secondary structural type. This result implies that higher prediction accuracies cannot be achieved relying solely on the amino acid composition of an unknown query protein as prediction input. Our prediction program SSCP has been made available as a World Wide Web and E-mail service.

Amino Acids↗

PubMed1991

On the computational approach to immobilized pH gradients.

The unified treatment for computing the pH of complex mixtures of mono- and polyprotic buffers, including ampholytes, as utilized in the gradient simulation program PGS, is presented. Its ability to compute pH, buffering power and ionic strength is shown by discussing a few simulations. The problems arising in the automatic formulation of optimal mixtures are presented, as well as the merits and limits of several target functions utilized in such optimizations. It is shown that no universal target function exists and that a proper optimization method should account for the fact that more than one formulation is possible for a given pH range.

Buffers↗

PubMed2004

A precise boundary element method for macromolecular transport properties.

A very precise boundary element numerical solution of the exact formulation of the hydrodynamic resistance problem with stick boundary conditions is presented. BEST, the Fortran 77 program developed for this purpose, computes the full transport tensors in the center of resistance or the center of diffusion for an arbitrarily shaped rigid body, including rotation-translation coupling. The input for this program is a triangulation of the solvent-defined surface of the molecule of interest, given by Connolly's MSROLL or other suitable triangulator. The triangulation is prepared for BEST by COALESCE, a program that allows user control over the quality and number of triangles to describe the surface. High numerical precision is assured by effectively exact integration of the Oseen tensor over triangular surface elements, and by scaling the hydrodynamic computation to the precise surface area of the molecule. Efficiency of computation is achieved by the use of public domain LAPACK routines that call BLAS Level 3 hardware-optimized subroutines available for most processors. A protein computation can be done in less than 10 min of CPU time in a modern Pentium IV processor. The present work includes a complete analysis of the sources of error in the numerical work and techniques to eliminate these errors. The operation of BEST is illustrated with applications to ellipsoids of revolution, and Lysozyme, a small protein. The typical numerical accuracy achieved is 0.05% compared to analytical theory. The numerical precision for a protein is better than 1%, much better than experimental errors in these quantities, and more than 10 times better than traditional bead-based methods.

Chemical Phenomena↗