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At least 1,621 records · Page 90Linked to original sources
PubMed2001

Fast LV motion estimation using subspace approximation techniques.

Cardiac motion estimation is very important in understanding cardiac dynamics and in noninvasive diagnosis of heart disease. Magnetic resonance (MR) imaging tagging is a technique for measuring heart deformations. In cardiac tagged MR images, a set of dark lines are noninvasively encoded within myocardial tissue providing the means for measurement of deformations of the heart. The points along tag lines measured in different frames and in different directions carry important information for determining the three-dimensional nonrigid movement of left ventricle. However, these measurements are sparse and, therefore, multidimensional interpolation techniques are needed to reconstruct a dense displacement field. In this paper, a novel subspace approximation technique is used to accomplish this task. We formulate the displacement estimation as a variational problem and then project the solution into spline subspaces. Efficient numerical methods are derived by taking advantages of B-spline properties. The proposed technique significantly improves our previous results reported in [3] with respect to computational time. The method is applied to a temporal sequence of two-dimensional images and is validated with simulated and in vivo heart data.

Algorithms↗
PubMed2004

Space-conserving optimal DNA-protein alignment.

DNA-protein alignment algorithms can be used to discover coding sequences in a genomic sequence, if the corresponding protein derivatives are known. They can also be used to identify potential coding sequences of a newly sequenced genome, by using proteins from related species. Previously known algorithms either solve a simplified formulation, or sacrifice optimality to achieve practical implementation. In this paper, we present a comprehensive formulation of the DNA-protein alignment problem, and an algorithm to compute the optimal alignment in O(mn) time using only four tables of size (m + 1) x (n + 1), where m and n are the lengths of the DNA and protein sequences, respectively. We also developed a Protein and DNA Alignment program PanDA that implements the proposed solution. Experimental results indicate that our algorithm produces high quality alignments.

Algorithms↗
PubMed2005

Needle steering and motion planning in soft tissues.

In this work, needle insertion into deformable tissue is formulated as a trajectory planning and control problem. A new concept of needle steering has been developed and a needle manipulation Jacobian defined using numerical needle insertion models that include needle deflection and soft tissue deformation. This concept is used in conjunction with a potential-field-based path planning technique to demonstrate needle tip placement and obstacle avoidance. Results from open loop insertion experiments are provided.

Animals↗
PubMed2004

Panoramic appearance-based recognition of video contents using matching graphs.

This paper proposes a general scheme for recognizing the contents of a video using a set of panoramas recorded in a database. In essence, a panorama inherently records the appearances of an omni-directional scene from its central point to arbitrary viewing directions and, thus, can serve as a compact representation of an environment. In particular, this paper emphasizes the use of a sequence of successive frames in a video taken with a video camera, instead of a single frame, for visual recognition. The associated recognition task is formulated as a shortest-path searching problem, and a dynamic-programming technique is used to solve it. Experimental results show that our method can effectively recognize a video.

Algorithms↗
PubMed2005

A full-wave Helmholtz model for continuous-wave ultrasound transmission.

A full-wave Helmholtz model of continuous-wave (CW) ultrasound fields may offer several attractive features over widely used partial-wave approximations. For example, many full-wave techniques can be easily adjusted for complex geometries, and multiple reflections of sound are automatically taken into account in the model. To date, however, the full-wave modeling of CW fields in general 3D geometries has been avoided due to the large computational cost associated with the numerical approximation of the Helmholtz equation. Recent developments in computing capacity together with improvements in finite element type modeling techniques are making possible wave simulations in 3D geometries which reach over tens of wavelengths. The aim of this study is to investigate the feasibility of a full-wave solution of the 3D Helmholtz equation for modeling of continuous-wave ultrasound fields in an inhomogeneous medium. The numerical approximation of the Helmholtz equation is computed using the ultraweak variational formulation (UWVF) method. In addition, an inverse problem technique is utilized to reconstruct the velocity distribution on the transducer which is used to model the sound source in the UWVF scheme. The modeling method is verified by comparing simulated and measured fields in the case of transmission of 531 kHz CW fields through layered plastic plates. The comparison shows a reasonable agreement between simulations and measurements at low angles of incidence but, due to mode conversion, the Helmholtz model becomes insufficient for simulating ultrasound fields in plates at large angles of incidence.

Algorithms↗
PubMed1992

Prophylactic nitrate therapy in angina pectoris--is there an optimal treatment regimen?

1. Nitrates have a place in the prophylactic treatment of patients with angina pectoris. Their efficacy is not in doubt. 2. However, there may be some practical problems associated with their use, such as unreliable absorption, short duration of action, treatment-induced headache, development of nitrate tolerance and a suggested rebound phenomenon observed during intermittent dosing. Furthermore, patient convenience with treatment schedule and patient compliance have to be considered during prophylactic treatment. The present article discusses how many of these problems may be solved by selection of formulation as well as nitrate compound. 3. The development of controlled-release formulations producing sufficiently high nitrate plasma concentration during part of the day followed by nitrate-poor rather than nitrate-free interval, have the potential to prevent both nitrate tolerance and rebound phenomenon, and produce a sufficiently long duration of action with a convenient once daily regimen.

Angina Pectoris↗
PubMed2006

Integrating science, practice and reflexivity--cognitive therapy with driving phobia.

The scientist-practitioner model has long been espoused within cognitive behavioural psychotherapy. The study includes an evaluation of the efficacy of cognitive therapy for driving phobia. Assessment, formulation and practical treatment of this common problem are also reported. Self-report measures evaluated results. Eight of the 10 consecutive cases improved significantly and reported that the intervention was acceptable. A reflexive analysis of the research findings and the influences on the first author's practice as a researcher and practitioner are also explored. Recommendations for future research are also made.

Accidents, Traffic↗
PubMed1985

The family void: treatment and theoretical aspects of the synchronous family paradigm.

The synchronous paradigm is a model of families whose members remain uninvolved and disconnected from each other yet somehow maintain relatively unvarying or even rigid patterns of behavior. In the synchronous paradigm, calm agreement and harmonious unity of action are valued above all. The concept of synchronous operation was first formulated by Constantine to solve certain theoretical problems growing out of the work of Kantor and Lehr. The theory has been elaborated upon through linkages established with other clinical and theoretical models of family dysfunction. Clinical experience in treating synchronous families has now contributed more detailed and practical understanding. Clinically, disabled synchronous families may present as bland, boring, or even death-like. They may have considerable difficulty accommodating to necessary developmental changes or to the demands of life crises, employing a variety of strategies to maintain the appearance of synchrony at the expense of adaptation. Their ability to ignore change and to absorb interventions can tax the abilities of even the most creative and energetic therapist. On the other hand, the quiet efficiency of the family and the social sensitivity of its members can be strong assets. Awareness of their strengths and special vulnerabilities can help the family therapist work more effectively with synchronous families.

Adolescent↗
PubMed1986

Sex differences in adolescent psychopathology.

The patterns of sex differences in psychiatric morbidity are reviewed and hypothesis for the empirical study formulated. Psychiatric treatment and registration for social problems are thoroughly examined in a prospective longitudinal study of a representative birth cohort of 6,482 adolescents. Mental health and psychiatric symptomatology are also checked by a questionnaire. The data obtained are analysed for males and females separately. The results clearly show that there are major sex differences in the pattern of psychopathology in adolescence. These differences are complex and seem related to sex role expectations among parents, adolescents and mental health professionals, and to social factors and the changes experienced in life. The results give some guidelines for the future development of psychiatric care for adolescents.

Adolescent↗
PubMedDate not supplied

The role of capillary forces in steady-state and transient seepage flows.

Steady and transient seepage problems were investigated numerically using a dimensionless formulation for water flow in variably saturated, two-dimensional anisotropic and homogenous porous media. The dimensionless formulation combines the aspect ratio and the anisotropy ratio in one dimensionless parameter, M, and accounts for capillarity effects using the ratio of the domain height to the height of capillary fringe as another dimensionless parameter, alpha. Two domain geometries were considered: rectangular and trapezoidal. It was found that M and alpha play major roles in the development and the height of the seepage face. The height of the steady-state seepage face increased with the decreasing value of alpha. The effects of capillarity on the development of the transient seepage face were investigated by lowering the open water level on one side of the domain at various uniform velocities while the other side was kept at a constant value. It was found for most scenarios that decoupling between the water table and the open water level first occurred for domains with large alpha. In other words, the seepage face heights of these systems were larger than those with a small alpha. These results are the opposite of the steady-state results and are due to the fact that drainage of the pores was the major mechanism controlling the drop of the transient water table, especially at earlier times. A criterion for the decoupling of the water table from the falling open water level (i.e., the formation of the transient seepage face) was developed by Dracos (1965). It states that decoupling does not occur as long as the falling speed, VF, of the open water level is less than Vd = K(o) sin2 B/phi where K(o) is the saturated hydraulic conductivity of the soil, phi is the porosity, and beta is the angle of the exit face with the horizontal (i.e., beta = pi/2 implies a vertical face). Our investigation revealed that decoupling occurs for smaller falling velocities than Vd, and is caused by, among others, the fact that the water table is not tangent to the exit face but rather intersects it at a nonzero angle.

Diffusion↗
PubMed1999

Modeling of polychromatic attenuation using computed tomography reconstructed images.

This paper presents a procedure for estimating an accurate model of the CT imaging process including spectral effects. As raw projection data are typically unavailable to the end-user, we adopt a post-processing approach that utilizes the reconstructed images themselves. This approach includes errors from x-ray scatter and the nonidealities of the built-in soft tissue correction into the beam characteristics, which is crucial to beam hardening correction algorithms that are designed to be applied directly to CT reconstructed images. We formulate this approach as a quadratic programming problem and propose two different methods, dimension reduction and regularization, to overcome ill conditioning in the model. For the regularization method we use a statistical procedure, Cross Validation, to select the regularization parameter. We have constructed step-wedge phantoms to estimate the effective beam spectrum of a GE CT-I scanner. Using the derived spectrum, we computed the attenuation ratios for the wedge phantoms and found that the worst case modeling error is less than 3% of the corresponding attenuation ratio. We have also built two test (hybrid) phantoms to evaluate the effective spectrum. Based on these test phantoms, we have shown that the effective beam spectrum provides an accurate model for the CT imaging process. Last, we used a simple beam hardening correction experiment to demonstrate the effectiveness of the estimated beam profile for removing beam hardening artifacts. We hope that this estimation procedure will encourage more independent research on beam hardening corrections and will lead to the development of application-specific beam hardening correction algorithms.

Algorithms↗
PubMed2004

Infinite-impulse-response models of the head-related transfer function.

Head-related transfer functions (HRTFs) measured from human subjects were approximated using infinite-impulse-response (IIR) filter models. Models were restricted to rational transfer functions (plus simple delays) so that specific models are characterized by the locations of poles and zeros in the complex plane. The all-pole case (with no nontrivial zeros) is treated first using the theory of linear prediction. Then the general pole-zero model is derived using a weighted-least-squares (WLS) formulation of the modified least-squares problem proposed by Kalman (1958). Both estimation algorithms are based on solutions of sets of linear equations and result in efficient computational schemes to find low-order model HRTFs. The validity of each of these two low-order models was assessed in psychophysical experiments. Specifically, a four-interval, two-alternative, forced-choice paradigm was used to test the discriminability of virtual stimuli constructed from empirical and model HRTFs for corresponding locations. For these experiments, the stimuli were 80 ms, noise tokens generated from a wideband noise generator. Results show that sounds synthesized through model HRTFs were indistinguishable from sounds synthesized from original HRTF measurements for the majority of positions tested. The advantages of the techniques described here are the computational efficiencies achieved for low-order IIR models. Properties of the all-pole and pole-zero estimators are discussed in the context of low-order HRTF representations, and implications for basic and applied contexts are considered.

Acoustics↗
PubMed2003

Vesicles in haptotaxis with hydrodynamical dissipation.

We analyze the problem of vesicle migration in haptotaxis (a motion directed by an adhesion gradient), though most of the reasoning applies to chemotaxis as well as to a variety of driving forces. A brief account has been published on this topic. We present an extensive analysis of this problem and provide a basic discussion of most of the relevant processes of migration. The problem allows for an arbitrary shape evolution which is compatible with the full hydrodynamical flow in the Stokes limit. The problem is solved within the boundary integral formulation based on the Oseen tensor. For the sake of simplicity we confine ourselves to 2D flows in the numerical analysis. There are basically two regimes (i) the tense regime where the vesicle behaves as a "droplet" with an effective contact angle. In that case the migration velocity is given by the Stokes law. (ii) The flask regime where the vesicle has a significant (on the scale of the vesicle size) contact curvature. In that case we obtain a new migration law which substantially differs from the Stokes law. We develop general arguments in order to extract analytical laws of migration. These are in good agreement with the full numerical analysis. Finally we mention several important future issues and open questions.

Adsorption↗
PubMed2006

Three-dimensional mechanical properties of porcine coronary arteries: a validated two-layer model.

The normal coronary artery consists of two mechanically distinct layers: intima-media and adventitia. The objective of this study is to establish a two-layer three-dimensional (3-D) stress-strain relation of porcine coronary arteries. Experimental measurements were made by a series of biaxial tests (inflation and axial extension) of intact coronary arteries and, subsequently, their corresponding intima-media or adventitia layer. The Fung-type exponential strain energy function was used to describe the 3-D strain-stress relation for each layer and the intact wall. A genetic algorithm was used to determine the material constants in the Fung-type constitutive equation by curve fitting the experimental data. Because one layer must be sacrificed before the other layer can be tested, the material property of the missing layer was computed from the material constants of the intact vessel and the tested layer. A total of 20 porcine hearts were used: one group of 10 hearts for the left anterior descending artery and another group of 10 hearts for the right coronary artery. Each group was further divided into two subgroups of five specimens tested for the intact wall and the intima-media layer and for the intact wall and the adventitia layer. Our results show statistically significant differences in the material properties of the two layers. The mathematical model was validated by experimental stress-strain data for individual layers. The validated 3-D constitutive model will serve as a foundation for formulation of layer-specific boundary value problems in coronary physiology and cardiology.

Algorithms↗
PubMed1979

Staff and patients evaluate their therapeutic community.

A committee of staff and patients conducted an informal evaluation of a therapeutic community on a 16-bed psychiatric unit. The committee reviewed the history, original intent, current purpose, and effectiveness of meetings held on the unit; when problems were identified, suggestions for change were formulated. The evaluation served to increase the efficiency of meetings and to counteract what the authors termed the "drift phenomenon," or the tendency of the original purpose or structure of a meeting to change over time. The process also fostered an atmosphere of mutual respect and an enhanced sense of purpose among the patients and staff who worked on the committee.

Attitude of Health Personnel↗
PubMed1992

Optimum nonlinear signal detection and estimation in the presence of ultrasonic speckle.

A unified approach to the design of nonlinear filters for speckle suppression in ultrasound B-mode images is presented. The detection of the (lesion) signal is formulated as a binary hypothesis-testing problem. The structure of the optimal decision rules is derived both in the case where the lesion signal is assumed either a constant or random variable. In the case of a constant signal, the maximum likelihood (ML) estimator and the optimal L-estimator are derived. In the case of a random lesion signal, the maximum a posteriori probability estimator of the lesion signal has also been found. Experimental results verify the superiority of the proposed ML-estimator and the L-estimator over the straightforward choice of an arithmetic mean for speckle filtering in simulated tissue mimicking phantom ultrasound B-mode images.

Equipment Design↗
PubMed2006

Development of a macrophage-based nanoparticle platform for antiretroviral drug delivery.

Complex dosing regimens, costs, side effects, biodistribution limitations, and variable drug pharmacokinetic patterns have affected the long-term efficacy of antiretroviral medicines. To address these problems, a nanoparticle indinavir (NP-IDV) formulation packaged into carrier bone marrow-derived macrophages (BMMs) was developed. Drug distribution and disease outcomes were assessed in immune-competent and human immunodeficiency virus type 1 (HIV-1)-infected humanized immune-deficient mice, respectively. In the former, NP-IDV formulation contained within BMMs was adoptively transferred. After a single administration, single-photon emission computed tomography, histology, and reverse-phase-high-performance liquid chromatography (RP-HPLC) demonstrated robust lung, liver, and spleen BMMs and drug distribution. Tissue and sera IDV levels were greater than or equal to 50 microM for 2 weeks. NP-IDV-BMMs administered to HIV-1-challenged humanized mice revealed reduced numbers of virus-infected cells in plasma, lymph nodes, spleen, liver, and lung, as well as, CD4(+) T-cell protection. We conclude that a single dose of NP-IDV, using BMMs as a carrier, is effective and warrants consideration for human testing.

Animals↗
PubMed2006

A classification-based framework for predicting and analyzing gene regulatory response.

BACKGROUND: We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called GeneClass. GeneClass is motivated by the hypothesis that in model organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular microarray experiment based on the presence of binding site subsequences ("motifs") in the gene's regulatory region and the expression levels of regulators such as transcription factors in the experiment ("parents"). GeneClass formulates the learning task as a classification problem--predicting +1 and -1 labels corresponding to up- and down-regulation beyond the levels of biological and measurement noise in microarray measurements. Using the Adaboost algorithm, GeneClass learns a prediction function in the form of an alternating decision tree, a margin-based generalization of a decision tree. METHODS: In the current work, we introduce a new, robust version of the GeneClass algorithm that increases stability and computational efficiency, yielding a more scalable and reliable predictive model. The improved stability of the prediction tree enables us to introduce a detailed post-processing framework for biological interpretation, including individual and group target gene analysis to reveal condition-specific regulation programs and to suggest signaling pathways. Robust GeneClass uses a novel stabilized variant of boosting that allows a set of correlated features, rather than single features, to be included at nodes of the tree; in this way, biologically important features that are correlated with the single best feature are retained rather than decorrelated and lost in the next round of boosting. Other computational developments include fast matrix computation of the loss function for all features, allowing scalability to large datasets, and the use of abstaining weak rules, which results in a more shallow and interpretable tree. We also show how to incorporate genome-wide protein-DNA binding data from ChIP chip experiments into the GeneClass algorithm, and we use an improved noise model for gene expression data. RESULTS: Using the improved scalability of Robust GeneClass, we present larger scale experiments on a yeast environmental stress dataset, training and testing on all genes and using a comprehensive set of potential regulators. We demonstrate the improved stability of the features in the learned prediction tree, and we show the utility of the post-processing framework by analyzing two groups of genes in yeast--the protein chaperones and a set of putative targets of the Nrg1 and Nrg2 transcription factors--and suggesting novel hypotheses about their transcriptional and post-transcriptional regulation. Detailed results and Robust GeneClass source code is available for download from http://www.cs.columbia.edu/compbio/robust-geneclass.

Algorithms↗