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PubMed2006

A mixed effects Markov model for repeated binary outcomes with non-ignorable dropout.

In many areas of research, repeated binary measures often represent a two-state stochastic process, where individuals can transition among two states. In a behavioural or physical disability setting, individuals can flow from susceptible or subthreshold state, to an infectious or symptomatic state, and back to a subthreshold state. Quite often the transition among the states happens in continuous time but is observed at discrete, irregularly spaced timepoints which may be unique to each individual. Methods for analyses of such data are typically based on the Markov assumption. Cook (Biometrics 1999; 55:915-920) introduced a conditional Markov model that accommodates the subject-to-subject variation in the model parameters with random effects. We extend this model by adding a non-ignorable dropout component to the model. Specification of the distribution of the random effects is made to guarantee a closed form expression of the marginal likelihood. This methodology is illustrated by applications to a data set from a parasitic field infection survey, a data set from a cocaine treatment study, and a data set from an aging study. Simulations suggest that the shared parameter model is robust with respect to at least one alternative non-ignorable model.

Activities of Daily Living↗
PubMed2005

Characterization of force chains in granular material.

It has been observed that the majority of particles in a granular material carries less than the average load and that the number of particles carrying larger than the average load decreases exponentially with increasing contact force. The particles carrying above average load appear to form a strong network of forces while the majority of particles belong to a weak network. The strong network of forces appear to have a spatial characteristic whereby the stronger forces are carried though chainlike particle groups referred to as force chains. There is a strong case for a connection between force chains of the discrete medium and the trajectory of the most compressive principal stress in its continuous idealization. While such properties seem obvious from descriptive analysis of physical and numerical experiments in granular media, progress in quantification of the force chain statistics requires an objective description of what constitutes a force chain. A procedure to quantify the occurrence of force chains is built on a proposed definition having two parts: first, the chain is a quasilinear arrangement of three or more particles, and second, along the chain, stress concentration within each grain is characterized by the vector delineating the most compressive principal stress. The procedure is incorporated into an algorithm that can be applied to large particle assemblies to compile force chain statistics. The procedure is demonstrated on a discrete element simulation of a rigid punch into a half space. It was found that only approximately half of the particles within the group of so-called strong network particles are part of force chains. Throughout deformation, the average length of force chains varied slightly but the number of force chains decreased as the punch advanced. The force chain lengths follow an exponential distribution. The procedure provides a tool for objective analysis of force chains, although future work is required to incorporate branching of force chains into the analysis.

Journal Article↗
PubMed2001

Stereotypic leg searching movements in the stick insect: kinematic analysis, behavioural context and simulation.

Insects are capable of efficient locomotion in a spatially complex environment, such as walking on a forest floor or climbing in a bush. One behavioural mechanism underlying such adaptability is the searching movement that occurs after loss of ground contact. Here, the kinematic sequence of leg searching movements of the stick insect Carausius morosus is analysed. Searching movements are shown to be stereotypic rhythmic movement sequences consisting of several loops. The typical loop structure allows the mean tarsus trajectory to be calculated using a feature-based averaging procedure. Thus, it is possible to describe the common underlying structure of this movement pattern. Phase relationships between joint angles, analysed for searching front legs, indicate a central role for the thorax-coxa joint in searching movements. Accordingly, the stereotyped loop structure of searching differs between front-, middle- and hindlegs, with leg-specific patterns being caused by differing protraction/retraction movements in the thorax-coxa joint. A simple artificial neural network that had originally been devised to generate simple swing movements allows two essential features of empirical searching trajectories to be simulated: (i) cyclic movements and (ii) the smooth transition into a search trajectory as a non-terminated swing movement. It is possible to generate several loops of a middle-leg search, but the precise size and shape of the loops fall short of a real-life approximation. Incorporation of front-leg retraction or hind-leg protraction during searching will also require an extension to the current model. Finally, front-leg searching occurs simultaneously with antennal movements. Also, because leg searching movements are a local behaviour, the legs remaining on the ground continue their stance phase, causing a forward shift of the body, including the searching leg. As a result of this shift, the centre of the searched space is close to the anterior extreme position of the tarsus during walking, representing the location of most likely ground contact according to past experience. Therefore, the behavioural relevance of searching movements arises from the combined actions of several limbs.

Animals↗
PubMed2006

Continuous time Markov models for binary longitudinal data.

Longitudinal data usually consist of a number of short time series. A group of subjects or groups of subjects are followed over time and observations are often taken at unequally spaced time points, and may be at different times for different subjects. When the errors and random effects are Gaussian, the likelihood of these unbalanced linear mixed models can be directly calculated, and nonlinear optimization used to obtain maximum likelihood estimates of the fixed regression coefficients and parameters in the variance components. For binary longitudinal data, a two state, non-homogeneous continuous time Markov process approach is used to model serial correlation within subjects. Formulating the model as a continuous time Markov process allows the observations to be equally or unequally spaced. Fixed and time varying covariates can be included in the model, and the continuous time model allows the estimation of the odds ratio for an exposure variable based on the steady state distribution. Exact likelihoods can be calculated. The initial probability distribution on the first observation on each subject is estimated using logistic regression that can involve covariates, and this estimation is embedded in the overall estimation. These models are applied to an intervention study designed to reduce children's sun exposure.

Biometry↗
PubMed1999

Implicit learning in 3D object recognition: the importance of temporal context.

A novel architecture and set of learning rules for cortical self-organization is proposed. The model is based on the idea that multiple information channels can modulate one another's plasticity. Features learned from bottom-up information sources can thus be influenced by those learned from contextual pathways, and vice versa. A maximum likelihood cost function allows this scheme to be implemented in a biologically feasible, hierarchical neural circuit. In simulations of the model, we first demonstrate the utility of temporal context in modulating plasticity. The model learns a representation that categorizes people's faces according to identity, independent of viewpoint, by taking advantage of the temporal continuity in image sequences. In a second set of simulations, we add plasticity to the contextual stream and explore variations in the architecture. In this case, the model learns a two-tiered representation, starting with a coarse view-based clustering and proceeding to a finer clustering of more specific stimulus features. This model provides a tenable account of how people may perform 3D object recognition in a hierarchical, bottom-up fashion.

Animals↗
PubMed2005

Spatial view cells in the hippocampus, and their idiothetic update based on place and head direction.

Single neuron recording studies have demonstrated the existence of spatial view neurons which encode information about the spatial location at which a primate is looking in the environment. These neurons are able to maintain their firing even in the absence of visual input. The standard neuronal network approach to model networks with memory that represent continuous spaces is that of continuous attractor neural networks. Stringer, Rolls and Trappenberg (2005) have recently shown how idiothetic (self-motion) inputs could update the activity packet of neuronal firing within a two-dimensional continuous attractor neural network of spatial view cells. However, this earlier study examined only the simplified situation in which the agent could rotate on the spot or move its eyes. In this paper we show how spatial view cells could be driven by head direction and place cells, themselves idiothetically updated. The head direction and place neurons are remapped by a competitive network with expansion recoding which self-organises so that different neurons represent different combinations of head direction and the place where the agent is located. The combination cells are then mapped by pattern association involving long-term synaptic potentiation but also long-term homosynaptic depression to spatial view cells, which during training are driven by the spatial view. After training, the spatial view cells are updated in the dark by the idiothetically driven head direction and place cells.

Animals↗
PubMed2000

An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance.

We have devised and implemented in PrISM (protein informatics system for modeling) a new measure of protein structural relationships, the protein structural distance (PSD). The PSD is designed to describe relationships between protein structures in quantitative rather than descriptive terms and is applicable both when two structures are very similar, and when they are very different. It is calculated with a structural alignment procedure that uses double dynamic programming to align secondary structure elements and an iterative rigid body superposition that minimizes the root-mean-square deviation of C(alpha) atoms. The alignment algorithm, as implemented on a modest workstation, is computationally efficient, allowing for large-scale structural comparisons. PSD scores for more than one and a half million pairs of proteins were calculated and compared to the discrete classification of proteins in the SCOP database. The PSD scores, which were obtained automatically, are in large part consistent with the manually derived classifications in SCOP. Discrepancies do arise, however, due, in part, to the fact that SCOP uses criteria other than structural similarity to derive classifications while the PrISM procedure is exclusively structure based. Analysis of PSD scores suggests that there is a continuous aspect of protein conformation space, even though various classification schemes are extremely useful. The use of a continuous measure for structural distance between all pairs of proteins allows us, as described in the two accompanying papers to derive sequence/structure relationships in a more quantitative way than has previously been possible. An important strength of the approach implemented in PrISM is its ability to address many different kinds of queries interactively, making its structural comparison procedure a convenient computational tool that complements structural classification databases such as SCOP and CATH.

Algorithms↗
PubMed2005

Multicanonical schemes for mapping out free-energy landscapes of single-component and multicomponent systems.

Multicanonical (MUCA) sampling is a powerful approach for simulating large domains of thermodynamic macrostate space that relies on mapping out either the density of states or a free energy of the system as a function of a suitable "order parameter." The purpose of this study is to extend and apply to more complex systems the method introduced in a previous paper [M. K. Fenwick and F. A. Escobedo, J. Chem. Phys. 120, 3066 (2004)] that uses Bennett's acceptance ratio method for estimating MUCA free energies. Four types of MUCA schemes are considered according to what order parameter is adopted and how the macrostate space is traversed: a la grand canonical ensemble, a la semigrand canonical ensemble, a la semigrand isothermal-isobaric ensemble, and a la isothermal-isobaric ensemble. Two types of systems are studied, the first is a two-component Lennard-Jones mixture that exhibits a vapor-liquid transition, and the second is a hard-cuboid containing system that exhibits an isotropic-liquid crystalline transition. These systems are simulated with different MUCA schemes and the resulting free-energy profiles are used to determine phase-coexistence conditions. For the Lennard-Jones systems, it is also demonstrated that different types of MUCA simulations can be conveniently performed over different macrostate regions and the results can be subsequently pieced together into a continuous weighting function.

Journal Article↗
PubMedDate not supplied

Simultaneous reconstruction, segmentation, and edge enhancement of relatively piecewise continuous images with intensity-level information.

A multinomial image model is proposed which uses intensity-level information for reconstruction of contiguous image regions. The intensity-level information assumes that image intensities are relatively constant within contiguous regions over the image-pixel array and that intensity levels of these regions are determined either empirically or theoretically by information criteria. These conditions may be valid, for example, for cardiac blood-pool imaging, where the intensity levels (or radionuclide activities) of myocardium, blood-pool, and background regions are distinct and the activities within each region of muscle, blood, or background are relatively uniform. To test the model, a mathematical phantom over a 64 x 64 array was constructed. The phantom had three contiguous regions. Each region had a different intensity level. Measurements from the phantom were simulated using an emission-tomography geometry. Fifty projections were generated over 180 degrees, with 64 equally spaced parallel rays per projection. Projection data were randomized to contain Poisson noise. Image reconstructions were performed using an iterative maximum a posteriori probability procedure. The contiguous regions corresponding to the three intensity levels were automatically segmented. Simultaneously, the edges of the regions were sharpened. Noise in the reconstructed images was significantly suppressed. Convergence of the iterative procedure to the phantom was observed. Compared with maximum likelihood and filtered-backprojection approaches, the results obtained using the maximum a posteriori probability with the intensity-level information demonstrated qualitative and quantitative improvement in localizing the regions of varying intensities.

Algorithms↗
PubMed2003

A distributed model of solid waste anaerobic digestion: sensitivity analysis.

A distributed model of anaerobic digestion of solid waste was developed to describe the balance between the rates of polymer hydrolysis and methanogenesis during the anaerobic conversion of rich and lean wastes in batch and continuous-flow reactors. Waste, volatile fatty acids (VFAs), methanogenic biomass and sodium concentrations are the model variables. Diffusion and advection of VFAs inhibiting both polymer hydrolysis and methanogenesis were considered. A sensitivity analysis by changing the key model parameter values was carried out. The model simulations showed that the effective distance between the areas of hydrolysis/acidogenesis and methanogenesis is very important. An initial spatial separation of rich waste and inoculum enhances the methane production and waste degradation at high waste loading if relatively low VFA diffusion into the methanogenic area is taking place. When both hydrolysis and methanogenesis are strongly inhibited by high levels of VFA, fluctuations in biomass concentration are thought to be responsible for initiating the expansion of methanogenic area over the reactor space.

Bacteria, Anaerobic↗
PubMed2003

A simple measure of correlation across time, frequency and space between continuous brain signals.

This paper introduces a simple but systematic method to estimate correlations between the spectral energy of two continuous electrophysiological signals in such a way that it can detect relationships between different frequencies and different latencies. From two series of signals (e.g. electroencephalogram, magnetoencephalogram or local field potentials) recorded from two sites in response to repeated sensory stimulations, the method computes the time-frequency energy of each signal. Then, it computes the Spearman rank order correlation coefficient across all the trials between the energy of the first signal series in one time-frequency region and the energy of the second signal series in a second time-frequency region. The method was designed to analyze interactions between frequency bands, in an effort to describe how the main brain rhythms interact with each other across time and space. It was applied to two simulations and to intracranial electro-encephalogram (EEG) recordings obtained from an epileptic patient performing two verbal discrimination tests (a phonological and a semantic task). It led to the identification of different correlations patterns in the gamma band depending on the level of semantic analysis performed by the patient.

Brain↗
PubMed2005

Mass-transfer limitations for nitrate removal in a uranium-contaminated aquifer.

A field test on in situ subsurface bioremediation of uranium(VI) is underway at the Y-12 National Security Complex in the Oak Ridge Reservation, Oak Ridge, TN. Nitrate has a high concentration at the site, which prevents U(VI) reduction, and thus must be removed. An acidic-flush strategy for nitrate removal was proposed to create a treatment zone with low levels of accessible nitrate. The subsurface at the site contains highly interconnected fractures surrounded by matrix blocks of low permeability and high porosity and is therefore subject to preferential flow and matrix diffusion. To identify the heterogeneous mass transfer properties, we performed a novel forced-gradient tracer test, which involved the addition of bromide, the displacement of nitrate, and the rebound of nitrate after completion of pumping. The simplest conceptualization consistent with the data is that the pore-space consists of a single mobile domain, as well as a fast and a slowly reacting immobile domain. The slowly reacting immobile domain (shale matrix) constitutes over 80% of the pore volume and acts as a long-term reservoir of nitrate. According to simulations, the nitrate stored in the slowly interacting immobile domain in the fast flow layer, at depths of about 12.2-13.7 m, will be reduced by an order of magnitude over a period of about a year. By contrast, the mobile domain rapidly responds to flushing, and a low average nitrate concentration can be maintained if the nitrate is removed as soon as it enters the mobile domain. A field-scale experiment in which the aquifer was flushed with acidic solution confirmed our understanding of the system. For the ongoing experiments on microbial U(VI) reduction, nitrate concentrations must be low in the mobile domain to ensure U(VI) reducing conditions. We therefore conclude that the nitrate leaching out of the immobile pore space must continuously be removed by in situ denitrification to maintain favorable conditions.

Bromides↗
PubMed2004

Swarm intelligence for mixed-variable design optimization.

Many engineering optimization problems frequently encounter continuous variables and discrete variables which adds considerably to the solution complexity. Very few of the existing methods can yield a globally optimal solution when the objective functions are non-convex and non-differentiable. This paper presents a hybrid swarm intelligence approach (HSIA) for solving these nonlinear optimization problems which contain integer, discrete, zero-one and continuous variables. HSIA provides an improvement in global search reliability in a mixed-variable space and converges steadily to a good solution. An approach to handle various kinds of variables and constraints is discussed. Comparison testing of several examples of mixed-variable optimization problems in the literature showed that the proposed approach is superior to current methods for finding the best solution, in terms of both solution quality and algorithm robustness.

Algorithms↗
PubMed2003

[Continuous target of China's manned space project and research direction of space medico-engineering].

The subject of space medico-engineering which takes manned space flight as its own task, played an important role in China's manned space project, and developed rapidly. According to China's next three manned space objectives: 1) to develop the technology of extra-vehicle activity (EVA) and test the astronauts' performance ability of EVA; 2) to develop the technology of docking with other object spacecraft in space; 3) to found a relatively large space lab, the research directions and key technology of space medico-engineering have been given, including astronaut's selection and training; requirements and evaluation of medicine and ergonomics of the space lab design; the researches of fields in astronauts' medical monitoring and space medicine; technology of environmental control and life support system in space module; technology of EVA or docking; and technology of simulation of astronaut's training.

Aerospace Medicine↗
PubMed2005

Systemic betamethasone accelerates functional recovery after a crush injury to rat sciatic nerve.

PURPOSE: The aim of the study was to evaluate the effect of perioperatively systemically administered betamethasone on nerve recovery (within or outside a confined space) after induced nerve crush injury. MATERIALS AND METHODS: The sciatic nerve of 40 adult Wistar rats was crushed. In half of the animals, the injured nerve was entrapped in a silicone tube to simulate the environment of a closed space, and in the other half the nerve was left to heal. Half of the rats in each group were treated with subcutaneous betamethasone (2 mg/kg body weight/day) during the first 24 hours, starting preoperatively, whereas the other half, the control animals, were given the same amount of physiological saline. All animals underwent preoperative and postoperative walking track analysis (toe spread [TS] and intermediate toe spread [ITS]) twice weekly for 6 weeks. RESULTS: For nonconfined space groups, there was no significant difference between the 2 groups (P = .052 for ITS and P = .315 for TS) during the first 2 weeks. Starting from the end of the second week, animals treated with betamethasone recovered more rapidly than did the controls (P < .001) and continued to do so until the end of the observation period. In the confined space groups, there was a significant difference between the 2 groups for ITS (P < .001) and for TS (P < .05) during the first 2 weeks. The difference continued at almost the same level of significance (P = .001) for ITS, whereas for TS, the difference disappeared after the second week. CONCLUSIONS: We conclude that short-term perioperative administration of betamethasone has a beneficial effect on the recovery of the injured rat sciatic nerve.

Animals↗
PubMed1993

Implantable cardioverter defibrillator electrogram recognition with a multilayer perceptron.

With the continuing development of new pacing and shock modalities, implantable cardioverter defibrillators must be able to recognize an increasingly wider range of arrhythmias so that therapy is delivered in an optimal way. Current rate-based systems can no longer meet this need. It is, therefore, necessary to develop new techniques that consider waveform morphology in addition to heart rate. Any developments, however, must be compatible with the strict power and space constraints imposed by implantable devices. Artificial neural networks offer a potentially viable way of meeting these objectives. In this article an artificial neural network based approach to the classification of arrhythmias from the ventricular intracardiac electrogram is described. It performs its classification on a set of easily extracted features that characterize waveform morphology and heart rate. Simulations showed that the artificial neural network performed better than a rate-based scheme similar to those used in some commercial devices.

Algorithms↗
PubMed2004

Power-law tails in nonstationary stochastic processes with asymmetrically multiplicative interactions.

We consider stochastic processes where randomly chosen particles with positive quantities x,y (>0) interact and exchange the quantities asymmetrically by the rule x(') =c [(1-a) x+by] , y(') =d [ax+(1-b) y] (x> or =y) , where (0< or =) a,b (< or =1) and c,d (>0) are interaction parameters. Noninteger power-law tails in the probability distribution function of scaled quantities are analyzed in a similar way as in inelastic Maxwell models. A transcendental equation to determine the growth rate gamma of the processes and the exponent s of the tails is derived formally from moment equations in Fourier space. In the case c=d or a+b=1 (a not = 0, 1) , the first-order moment equation admits a closed form solution and gamma and s are calculated analytically from the transcendental equation. It becomes evident that at c=d , exchange rate b of small quantities is irrelevant to power-law tails. In the case c not = d and a+b not = 1 , a closed form solution of the first-order moment equation cannot be obtained because of asymmetry of interactions. However, the moment equation for a singular term formally forms a closed solution and possibility for the presence of power-law tails is shown. Continuity of the exponent s with respect to parameters a,b,c,d is discussed. Then numerical simulations are carried out and compared with the theory. Good agreement is achieved for both gamma and s.

Journal Article↗
PubMedDate not supplied

Psychological and psychophysiological factors in prevention and treatment of cold injuries.

Cold injured patients in Alaska come from many sources. Although sport and work continues to provide large numbers of cold injured, most severe repeat injuries tend to reflect other biopsychosocial consequences. Certain behaviors can increase the probability of injury, however all persons living in cold climates are potential candidates. One can decrease risk by education, knowledge and intelligent behavior. Proper respect for adequate protection and hydration seem to be critical factors. Understanding the psychological, physiological and psychophysiological aspects of the cold environment performer helps refine the prevention and treatment strategies for cold injury. Skill training with bio-behavioral methods, such as thermal biofeedback, and the value of medical psychotherapy appear to offer continued promise by facilitating physiologic recovery from injury, as well as assisting in long term rehabilitation. Both approaches increase the likelihood of a favorable healing response by soliciting active patient participation. Medical Psychotherapy for traumatic injuries can also help identify and manage cognitive emotional issues for families and patients faced with the permanent consequences of severe thermal injuries. Thermal biofeedback therapy has the potential benefit of encouraging greater self-reliance and responsibility for self-regulating overall health by integrating self-management skills regarding physiology, diet and lifestyle. Inpatient and outpatient biofeedback training offers specific influence over vascular responses for healing, as well as providing an effective tool for pain management. Interest in cold region habitation has continued to expand our study of human tolerance to harsh, extreme environments. Biological, psychological, sociological, and anthropological views on adaptation, habituation, acclimatization, and injury in cold environments acknowledges the role of development, learning and educated responses to cold environments. The study of health, performance, and injury prevention in extreme isolated cold environments has important strategic and scientific implications. What is learned from behavioral studies of cold survival provides an opportunity to increase our scientific knowledge and understanding. These cold research findings can assist in our future exploration of cold, underwater farming at great depths, and to far distance space travel to cold planets. The relatively new research frontier "Polar Psychology" has evolved to study how interactions with cold environments can have both positive and/or negative consequences. This research simulates the psychological factors likely to be encountered while exploring isolated cold regions of distant galaxies. The psychological and psychophysiological correlates of cold experience appear to be a function of four interactive issues: the environment, genetic predisposition, learning or experience, and finally perception or cognition. Individual cold tolerance seems to relate heavily on sensation, perception and behavior.(ABSTRACT TRUNCATED AT 400 WORDS)

Acclimatization↗