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PubMed2026

Proportionality-based association metrics in count compositional data.

Compositional data comprise vectors that describe the constituent parts of a whole. Data arising from various -omics platforms such as 16S and RNA sequencing are compositional in nature. In this kind of data, correlations between features on raw counts have no meaningful interpretation. Metrics of proportionality were formulated to address this problem. However, an inherent bias arises when these metrics are calculated empirically on count-based measures due to variability in read depths. We quantify the bias introduced by empirically calculating proportionality-based association metrics in count data. Additionally, we propose a means of estimating these metrics within a logit-normal multinomial model in pursuit of more accurate estimates. The model-based estimates are shown to outperform empirical estimates in simulated data and are applied to a mouse embryonic stem cell single-cell sequencing dataset, as well as a pediatric-onset multiple sclerosis metagenomic dataset.

Animals↗
PubMed2003

Spontaneous periodic distortions in nematic liquid crystals: dependence on the tilt angle.

The possibility of spontaneous periodic distortions, depending on the tilt angle in a nematic liquid crystal sample, is investigated by means of a general formulation of the stability problem. It is shown that due to the presence of a surfacelike term in the free-energy density, the uniform pattern can be destabilized, giving rise to a periodic distortion of the director. Our analysis establishes, in general terms, the conditions for the formation of stable periodic structures in nematic samples. In particular, we determine the wavelengths for which the periodic distortion exists by investigating its dependence on the tilt angle, characterizing the uniform pattern, and on the saddle-splay elastic constant. The effect considered in our paper is a finite size effect, related to the slab geometry of the nematic sample under consideration.

Journal Article↗
PubMed2003

Optical bistability involving photonic crystal microcavities and Fano line shapes.

The reflectivity of a single-channel waveguide mode upon resonantly coupling to a Kerr-active nonlinear resonant cavity is calculated analytically, including the effects of two-photon absorption. The resonant reflectivity takes the form of a Fano resonance because the solution includes linear reflections from perturbations downstream of the localized cavity. Instead of using a Hamiltonian formulation of the scattering problem, an intuitive set of basis states is used to expand the Green's function of the electric field wave equation. All resulting overlap functions describing the linear coupling between guided and localized states, and the nonlinear renormalization of the material's refractive index, are in terms of well-defined physical quantities. Although derived in the context of photonic crystal-based waveguides and cavities, the treatment is valid for any low-loss waveguide-resonator geometry that satisfies specific weak coupling criteria. For a cavity consisting of Al0.18Ga0.82As, hosting a localized mode at 1.55 microm with a Q of 4000 and a mode volume of 0.055 microm(3), we predict the onset of bistable reflection at incident powers of approximately 40 mW. The downstream reflections lead to hysteresis loops in the reflectivity that are topologically distinct from conventional Lorentzian-derived loops characteristic of isolated Fabry-Perot cavities. We provide a stability argument that reveals the unstable branches of these unique hysteresis loops, and we illustrate some of the rich bistable behaviors that can be engineered with such downstream sources.

Journal Article↗
PubMed2004

Geometric constant defining shape transitions of carbon nanotubes under pressure.

We demonstrate that when a single-walled carbon nanotube is under pressure it undergoes a series of shape transitions, first transforming from a circle to an oval and then from an oval to a peanut. Most remarkably, the ratio of the area of the tube cross sections at the second transition over that at the first transition appears as a constant, independent of the tube radius. Its accurate value is computed to be G=0.819 469, by formulating a variational geometry problem to represent single-walled carbon nanotubes with a family of closed plane curves of fixed length and minimum bending energy. The implications of such a geometric constant in designing nanotube electromechanical pressure sensors are discussed.

Journal Article↗
PubMed2005

Nonlinear screening theory of the Coulomb glass.

A nonlinear screening theory is formulated to study the problem of gap formation and its relation to glassy freezing in classical Coulomb glasses. We find that a pseudogap ("plasma dip") in a single-particle density of states begins to open already at temperatures comparable to the Coulomb energy. This phenomenon is shown to reflect the emergence of short-range correlations in a liquid (plasma) phase, a process which occurs even in the absence of disorder. Glassy ordering emerges when disorder is present, but this occurs only at temperatures roughly an order of magnitude lower. Our result demonstrate that the formation of the plasma dip at high temperatures is a process distinct from the formation of the Efros-Shklovskii pseudogap, which in our model emerges only within the glassy phase.

Journal Article↗
PubMed2000

Solving the Sayre equation by simulated annealing

Simulated annealing is used to solve the Sayre equation formulated as a minimization problem. Trial calculations for structures containing up to 126 non-H equal atoms have been carried out. The residual as a function of the fictitious temperature always exhibits a sudden drop before the emergence of the correct structure at low temperature. This behavior casts doubt on the suitability of solving the Sayre equation by steepest-descent methods.

Journal Article↗
PubMed1997

A new method for myocardial activation imaging.

Noninvasive images of the myocardial activation sequence are acquired, based on a new formulation of the inverse problem of electrocardiography in terms of the critical points of the ventricular surface activation map. It is shown that the method is stable with respect to substantial amounts of correlated noise common in the measurements and modeling of electrocardiography and that problems associated with conventional regularization techniques can be circumvented. Examples of application of the method to measured human data are presented. This first invasive validation of results compares well to previously published results obtained by using a standard approach. The method can provide additional constraints on, and thus improve, traditional methods aimed at solving the inverse problem of electrocardiography.

Algorithms↗
PubMed2001

Hierarchical estimation of a dense deformation field for 3-D robust registration.

A new method for medical image registration is formulated as a minimization problem involving robust estimators. We propose an efficient hierarchical optimization framework which is both multiresolution and multigrid. An anatomical segmentation of the cortex is introduced in the adaptive partitioning of the volume on which the multigrid minimization is based. This allows to limit the estimation to the areas of interest, to accelerate the algorithm, and to refine the estimation in specified areas. At each stage of the hierarchical estimation, we refine current estimate by seeking a piecewise affine model for the incremental deformation field. The performance of this method is numerically evaluated on simulated data and its benefits and robustness are shown on a database of 18 magnetic resonance imaging scans of the head.

Computer Simulation↗
PubMed2005

Generalizing Swendsen-Wang to sampling arbitrary posterior probabilities.

Many vision tasks can be formulated as graph partition problems that minimize energy functions. For such problems, the Gibbs sampler provides a general solution but is very slow, while other methods, such as Ncut and graph cuts are computationally effective but only work for specific energy forms and are not generally applicable. In this paper, we present a new inference algorithm that generalizes the Swendsen-Wang method to arbitrary probabilities defined on graph partitions. We begin by computing graph edge weights, based on local image features. Then, the algorithm iterates two steps. 1) Graph clustering: It forms connected components by cutting the edges probabilistically based on their weights. 2) Graph relabeling: It selects one connected component and flips probabilistically, the coloring of all vertices in the component simultaneously. Thus, it realizes the split, merge, and regrouping of a "chunk" of the graph, in contrast to Gibbs sampler that flips a single vertex. We prove that this algorithm simulates ergodic and reversible Markov chain jumps in the space of graph partitions and is applicable to arbitrary posterior probabilities or energy functions defined on graphs. We demonstrate the algorithm on two typical problems in computer vision--image segmentation and stereo vision. Experimentally, we show that it is 100-400 times faster in CPU time than the classical Gibbs sampler and 20-40 times faster then the DDMCMC segmentation algorithm. For stereo, we compare performance with graph cuts and belief propagation. We also show that our algorithm can automatically infer generative models and obtain satisfactory results (better than the graphic cuts or belief propagation) in the same amount of time.

Algorithms↗
PubMed2002

A cacophony of theories: contributions towards a story-based understanding of analytic treatments.

The article addresses problems associated with analytic formulations from the founders of psychoanalysis, including C. G. Jung. Although no longer able to claim a scientific basis for these theoretical constructs, analytic practitioners still use this outdated terminology when presenting their work with patients. By now there is a cacophony of theories often concealing rather than explaining. Denial of loneliness, notions of special knowledge, and idealization of the 'The Founder' seem to perpetuate formulations which no longer carry a clear meaning. The article explores three proposals for describing analytic treatments based on the works of the psychoanalyst Roy Schafer and the cognitive psychologist Roger Schank: analytic attitudes, therapeutic narratives and specific treatment perspectives. The first addresses findings from psychotherapy research about the centrality of analytic attitudes. The second applies the findings about story-based memory and narratives to therapy relationships, and the third takes note of the fact that analytic attention often is more complex than can be described with terms such as transference/countertransference.

Cognition↗
PubMed1993

Factors affecting the availability of sugar-free medicines for children--a survey in the UK.

Because use of sugar-containing paediatric medicines is an aetiological factor in dental caries, sugar-free alternatives are slowly becoming more readily available. However, it is claimed that, for a variety of reasons, their production is difficult. This investigation was undertaken to determine whether problems exist in the formulation, production and availability of sugar-free medicines. A structured questionnaire was used with personnel involved in the production, marketing and wholesaling of paediatric medicines in the UK. Information was obtained from interviews with, or from questionnaires completed by, personnel of five pharmaceutical and five wholesale companies. The findings indicated that the only obstacle to producing sugar-free medicines is slightly higher cost, and that manufacturers are influenced to change mainly by consumer pressure. It was concluded that the dental profession should advise the public to demand sugar-free medicines and doctors to prescribe them.

Child↗
PubMed1992

Chinese medical school exit objectives: a multi-institutional survey of teacher opinion.

This paper describes a collaborative survey of Chinese medical school teacher opinion concerning clinical behaviours and skills that Chinese students should be expected to demonstrate prior to graduation from medical school. Selected teachers from four Chinese medical schools indicated whether each of 77 objectives was: essential for every student to know or demonstrate prior to graduation; useful but not essential; or not applicable to their educational programmes. Results show teachers' expectations regarding some of the behaviours and skills Chinese medical school teachers consider to be important for students to learn. Forty-nine per cent of the exit objectives were regarded as essential by 75% or more of the teachers. The most essential objectives involved performing clinical procedures, collaborating and communicating with health care professionals, conducting organ system examinations, formulating hypotheses and defining problems. Other essential objectives were concerned with communicating with patients and their families, maintaining currency within the discipline, and recognition, evaluation and triage of patients with life-threatening or chronic conditions. Exit objectives related to health promotion and risk assessment were regarded as useful but not essential at the undergraduate level. Implications for Chinese medical education are discussed.

China↗
PubMed1998

Postoperative care following carbon dioxide laser resurfacing. Avoiding pitfalls.

Facial skin resurfacing using the carbon dioxide laser has become an increasingly popular procedure. Improvements in carbon dioxide laser technology have made the procedure simpler and more reliable. However, difficulties and problems in the postoperative period can lead to patient morbidity and physician anxiety. The authors have performed laser resurfacing in almost 2,000 patients in the last 4 years. Problems encountered and methods formulated to minimize postoperative complications are discussed.

Dermatologic Surgical Procedures↗
PubMed1992

Cultural and integrative therapy issues in the treatment of a Jamaican woman with panic disorder.

This article examines the treatment of a Jamaican woman with panic disorder, with a specific focus on the role of culture and the use of multiple formulations of the clinical problem. The work suggests that complex decisions are sometimes called for in assessing whether treatment should advocate against a cultural norm of the clients. The work further suggests that conceptualization of the problem from the vantage point of multiple frameworks is warranted in some instances, but that it requires considerable thought in order to achieve an integrated, coherent treatment plan.

Adult↗
PubMed1996

A counter current vascular network model of heat transfer in tissues.

A fully conjugated blood vessel network model (FCBVNM) for calculating tissue temperatures has been developed, tested, and studied. This type of model represents a more fundamental approach to modeling temperatures in tissues than do the generally used approximate equations such as the Pennes'BHTE or effective thermal conductivity equations. As such, this type of model can be used to study many important questions at a more basic level. For example, in the particular hyperthermia application studied herein, a simple vessel network model predicts that the role of counter current veins is minimal and that their presence does not significantly affect the tissue temperature profiles: the arteries, however, removed a significant fraction of the power deposited in the tissue. These more fundamental models can also be used to check the validity of approximate equations. For example, using the present simple model, when the temperatures calculated by the FCBVNM are used for comparing predictions from two approximation equations (a simple effective thermal conductivity and a simple Pennes' bio-heat transfer equation formulation of the same problem) it is found that the Pennes' equation better approximates the FCBVNM temperatures than does the k(eff) model. These results also show that the "perfusion" value (W) in the Pennes' BHTE is not necessarily equal to the "true" tissue perfusion (P) as calculated from mass flow rate considerations, but can be greater than, equal to, or less than that value depending on (1) how many vessel levels are modeled by the BHTE, and (2) the "true" tissue perfusion magnitude. This study uses a simple, generic vessel network model to demonstrate the potential usefulness of such fully conjugated vessel network models, and the associated need for developing and applying more complicated and realistic vascular network models. As more realistic vascular models (vessel sizes, orientations, and flow rates) are developed, the predictions of the fully conjugated models should more closely model and approach the true tissue temperature distributions, thus making these fully conjugated models more accurate and valuable tools for studying tissue heat transfer processes.

Animals↗
PubMed1993

Biomechanics of diarthrodial joints: a review of twenty years of progress.

A survey of some of the advances made over the past twenty years in understanding diarthrodial joint biomechanics is presented. Topics covered in this review include: biotribology (i.e., friction, lubrication and wear of diarthrodial joints); contact area determinations; stereophotogrammetric rendering of articular surfaces; deformational field analysis using canonical problems; and finite element formulations for both infinitesimal and finite deformations of biphasic materials and precise anatomic surfaces. Suggestions are made for future research directions as well.

Animals↗
PubMed2002

A full 3D plane-wave-expansion model for 1-3 piezoelectric composite structures.

The plane-wave-expansion (PWE) approach dedicated to the simulation of periodic devices has been extended to 1-3 connectivity piezoelectric composite structures. The case of simple but actual piezoelectric composite structures is addressed, taking piezoelectricity, acoustic losses, and electrical excitation conditions rigorously into account. The material distribution is represented by using a bidimensional Fourier series and the electromechanical response is simulated using a Bloch-Floquet expansion together with the Fahmy-Adler formulation of the Christoffel problem. Application of the model to 1-3 connectivity piezoelectric composites is reported and compared to previously published analyses of this problem.

Journal Article↗