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PubMed1997

Generation of fractals from incursive automata, digital diffusion and wave equation systems.

This paper describes modelling tools for formal systems design in the fields of information and physical systems. The concept and method of incursion and hyperincursion are first applied to the fractal machine, an hyperincursive cellular automata with sequential computations with exclusive or where time plays a central role. Simulations show the generation of fractal patterns. The computation is incursive, for inclusive recursion, in the sense that an automaton is computed at future time t + 1 as a function of its neighbouring automata at the present and/or past time steps but also at future time t + 1. The hyperincursion is an incursion when several values can be generated for each time step. External incursive inputs cannot be transformed to recursion. This is really a practical example of the final cause of Aristotle. Internal incursive inputs defined at the future time can be transformed to recursive inputs by self-reference defining then a self-referential system. A particular case of self-reference with the fractal machine shows a non deterministic hyperincursive field. The concepts of incursion and hyperincursion can be related to the theory of hypersets where a set includes itself. Secondly, the incursion is applied to generate fractals with different scaling symmetries. This is used to generate the same fractal at different scales like the box counting method for computing a fractal dimension. The simulation of fractals with an initial condition given by pictures is shown to be a process similar to a hologram. Interference of the pictures with some symmetry gives rise to complex patterns. This method is also used to generate fractal interlacing. Thirdly, it is shown that fractals can also be generated from digital diffusion and wave equations, that is to say from the modulo N of their finite difference equations with integer coefficients.

Computer Simulation↗
PubMed2005

The EpiLink record linkage software: presentation and results of linkage test on cancer registry files.

OBJECTIVES: Record linkage, the process of bringing together separately compiled but related records from different databases, is essential in many areas of biomedical research. We developed a record linkage program (EpiLink), which employs a simple mathematical approach. We describe the program and present results obtained testing it in a linkage task. METHODS: EpiLink was designed to be flexible with user-friendly settings to tailor linkage and operating parameters to specific linkage tasks, and employ deterministic, probabilistic or sequential deterministic-probabilistic linkage strategies as required. The user can also standardize data format, examine linkage results and accept or discard them. We used EpiLink to link a subset of cases of the Lombardy Cancer Registry (20,724 records) with the Social Security file of the population (1,021,846 records) covered by the registry. The linkage strategy was deterministic, followed by several probabilistic linkage steps. RESULTS: Manual inspection of the results showed that EpiLink achieved 98.8% specificity and 96.5% sensitivity. CONCLUSIONS: EpiLink is a practical and accurate means of linking records from different databases that can be used by non-statisticians and is efficient in terms of human and financial resources.

Humans↗
PubMed1995

From passive diffusion to active cellular migration in mathematical models of tumour invasion.

Mathematical models of tumour invasion appear as interesting tools for connecting the information extracted from medical imaging techniques and the large amount of data collected at the cellular and molecular levels. Most of the recent studies have used stochastic models of cell translocation for the comparison of computer simulations with histological solid tumour sections in order to discriminate and characterise expansive growth and active cell movements during host tissue invasion. This paper describes how a deterministic approach based on reaction-diffusion models and their generalisation in the mechano-chemical framework developed in the study of biological morphogenesis can be an alternative for analysing tumour morphological patterns. We support these considerations by reviewing two studies. In the first example, successful comparison of simulated brain tumour growth with a time sequence of computerised tomography (CT) scans leads to a quantification of the clinical parameters describing the invasion process and the therapy. The second example considers minimal hypotheses relating cell motility and cell traction forces. Using this model, we can simulate the bifurcation from an homogeneous distribution of cells at the tumour surface toward a nonhomogeneous density pattern which could characterise a pre-invasive stage at the tumour-host tissue interface.

Brain↗
PubMed2006

Aging, working memory, and discrimination learning.

Older adults easily learn probabilistic relationships between cues and outcomes when the predictive event is the occurrence of a cue, but have greater difficulty when the predictive event is the nonoccurrence of a cue (Mutter & Pliske, 1996; Mutter & Plumlee, 2004; Mutter & Williams, 2004). This study explored whether this age-related deficit occurs in a simpler learning context and whether it might be related to working memory (WM) decline. We gave younger and older adults simultaneous discrimination tasks that allowed us to compare their ability to learn deterministic relationships when either the occurrence (feature positive; FP) or the nonoccurrence (feature negative; FN) of a distinctive feature predicted reinforcement. We also included a group of younger adults who performed the discrimination tasks under a concurrent WM load. Both age and WM load had a detrimental effect on initial FP and FN discrimination; however, these effects persisted only in FN discrimination after additional learning experience. Learning predictive relationships requires inductive reasoning processes that apparently do not operate as efficiently in individuals with reduced WM capacity. The impact of WM decline may ultimately be greater for negative cue-outcome relationships because learning these relationships requires more difficult inductive reasoning processes, which place greater demands on WM.

Adult↗
PubMed2000

Evolution proposes and ontogeny disposes.

Genes, the basic building blocks of evolution, are highly conserved. For example, the mouse and human have approximately the same number of genes, and around 94% are identical in the two species. Since species differ on multiple dimensions (e.g., anatomy, physiology, and behavior), it follows that identical genes may subserve different functions in different species. Two reasons for this are gene-gene interaction and gene-environment interaction (and it is the presence of these interactions which prevents one from making deterministic statements about genetics, thus rendering obsolete the nature-nurture controversy). Behavioral examples of both types of interactions are presented, including studies showing that (1) the uterine environment enhances later cognitive competence, (2) early postnatal experiences affect learning and emotionality and can extend into future generations, (3) maternal behavior changes the offspring's later behavior and physiology, and (4) knocking out one gene results in an animal less competent in one learning process but more competent in a complementary learning process.

Animals↗
PubMedDate not supplied

Computational dosimetry and treatment planning considerations for neutron capture therapy.

Specialized treatment planning software systems are generally required for neutron capture therapy (NCT) research and clinical applications. The standard simplifying approximations that work well for treatment planning computations in the case of many other modalities are usually not appropriate for application to neutron transport. One generally must obtain an explicit three-dimensional numerical solution of the governing transport equation, with energy-dependent neutron scattering completely taken into account. Treatment planning systems that have been successfully introduced for NCT applications over the past 15 years rely on the Monte Carlo stochastic simulation method for the necessary computations, primarily because of the geometric complexity of human anatomy. However, historically, there has also been interest in the application of deterministic methods, and there have been some practical developments in this area. Most recently, interest has turned toward the creation of treatment planning software that is not limited to any specific therapy modality, with NCT as only one of several applications. A key issue with NCT treatment planning has to do with boron quantification, and whether improved information concerning the spatial biodistribution of boron can be effectively used to improve the treatment planning process. Validation and benchmarking of computations for NCT are also of current developmental interest. Various institutions have their own procedures, but standard validation models are not yet in wide use.

Boron Compounds↗
PubMed2004

Deterministic quantum teleportation with atoms.

Teleportation of a quantum state encompasses the complete transfer of information from one particle to another. The complete specification of the quantum state of a system generally requires an infinite amount of information, even for simple two-level systems (qubits). Moreover, the principles of quantum mechanics dictate that any measurement on a system immediately alters its state, while yielding at most one bit of information. The transfer of a state from one system to another (by performing measurements on the first and operations on the second) might therefore appear impossible. However, it has been shown that the entangling properties of quantum mechanics, in combination with classical communication, allow quantum-state teleportation to be performed. Teleportation using pairs of entangled photons has been demonstrated, but such techniques are probabilistic, requiring post-selection of measured photons. Here, we report deterministic quantum-state teleportation between a pair of trapped calcium ions. Following closely the original proposal, we create a highly entangled pair of ions and perform a complete Bell-state measurement involving one ion from this pair and a third source ion. State reconstruction conditioned on this measurement is then performed on the other half of the entangled pair. The measured fidelity is 75%, demonstrating unequivocally the quantum nature of the process.

Journal Article↗
PubMed2004

Perceptions on the standardization of psychiatric work: development of a care pathway.

Policy development and practice for hospital care has shifted towards a more deterministic approach. Crucial within this development is the assumption that interventions can be standardized to fit within the confines of a practice framework. A system to deliver standardized approaches to care is a care pathway. A research study was carried out to determine how care could be standardized to fit within a care pathway for people diagnosed with schizophrenia. A range of interviews with the multidisciplinary team and observations of the working group process was the data collection technique. Analysis was driven by emergent themes across the data set. Clinicians expressed divergent views on the nature of standardized care for people with schizophrenia. Respondents also offered a deeper understanding of standardized care by arguing for a sense of flexibility to be built into care systems. Findings from this study have implications for the introduction of NICE core standards for people with schizophrenia. For example, clinicians may be so opposed to such structures as to work against them. By understanding different views on standardized care, it may ultimately support their introduction into practice.

Attitude of Health Personnel↗
PubMed2001

Dynamics of the level of deterministic chaos associated with gastric electrical uncoupling in dogs.

This study investigated the impact of gastric electrical uncoupling on the dynamics of the level of deterministic chaos in cutaneous gastric electrical signals. Eight-channel electrogastrograms (EGG) were recorded from 16 unconscious dogs. Controlled gastric electrical uncoupling was introduced by circumferentially cutting the whole gastric muscle at two different locations. Three separate 30-min EGG recordings were obtained from each dog in the three different states (basal, after the first cut, and after the second cut). The Lyapunov exponents were calculated from sixteen 6.31-min intervals with 75% overlap obtained from each channel in each state. Inadequate EGG signals from which the Lyapunov exponent could not be reliably calculated were quantitatively discarded. The variance and the standard deviation of the three Lyapunov exponent distributions obtained from each channel were studied, and the mean values were subjected to a Student t-test. In 65.6% of all studied channels, the level of chaos was significantly different (p< 0.01) after the first cut compared to the basal state, but no predominant direction of variation was observed (47. 7% increment vs. 52.5% decrement). After the second cut, 63.6% of the channels studied showed significantly greater Lyapunov exponent compared to the basal state, and 63.1% exhibited significantly greater (p< 0.01) level of chaos compared to the intercut state. The dynamics of the level of deterministic chaos in canine electrogastrograms is highly sensitive to severe gastric electrical uncoupling. Moreover, some channel configurations seem to be more sensitive than others in detecting uncoupling.

Animals↗
PubMed2006

Stochastic stable population growth in integral projection models: theory and application.

Stochastic matrix projection models are widely used to model age- or stage-structured populations with vital rates that fluctuate randomly over time. Practical applications of these models rest on qualitative properties such as the existence of a long term population growth rate, asymptotic log-normality of total population size, and weak ergodicity of population structure. We show here that these properties are shared by a general stochastic integral projection model, by using results in (Eveson in D. Phil. Thesis, University of Sussex, 1991, Eveson in Proc. Lond. Math. Soc. 70, 411-440, 1993) to extend the approach in (Lange and Holmes in J. Appl. Prob. 18, 325-344, 1981). Integral projection models allow individuals to be cross-classified by multiple attributes, either discrete or continuous, and allow the classification to change during the life cycle. These features are present in plant populations with size and age as important predictors of individual fate, populations with a persistent bank of dormant seeds or eggs, and animal species with complex life cycles. We also present a case-study based on a 6-year field study of the Illyrian thistle, Onopordum illyricum, to demonstrate how easily a stochastic integral model can be parameterized from field data and then applied using familiar matrix software and methods. Thistle demography is affected by multiple traits (size, age and a latent "quality" variable), which would be difficult to accommodate in a classical matrix model. We use the model to explore the evolution of size- and age-dependent flowering using an evolutionarily stable strategy (ESS) approach. We find close agreement between the observed flowering behavior and the predicted ESS from the stochastic model, whereas the ESS predicted from a deterministic version of the model is very different from observed flowering behavior. These results strongly suggest that the flowering strategy in O. illyricum is an adaptation to random between-year variation in vital rates.

Ecosystem↗
PubMed2006

Patient dosimetry in diagnostic and interventional radiology: a practical approach using trigger levels.

Patient dosimetry is performed in radiology and interventional radiology to assess whether deterministic injuries may occur and to establish the risk of stochastic effects. A fundamental problem for patient dosimetry is that no single quantity can be used to accurately assess both the risk of stochastic effects and whether deterministic injuries will occur following a specific examination or procedure. In cardiology and interventional radiology, two different approaches to patient dosimetry are commonly used. Effective dose is a quantity which correlates reasonably well with the risk of stochastic effects. Effective dose may be deduced from the dose-area product (DAP) for the procedure if sufficient information is known. DAP does not correlate with maximum skin dose, which may be used to predict whether deterministic injuries may occur. DAP meter readings may be used as a trigger level for the investigation of maximum skin entrance dose. Trigger levels for different procedures are proposed.

Humans↗
PubMed1999

Attractor control of the redox reactions of bovine cytochrome c.

Although the conformational changes accompanying the oxidation of ferrocytochrome c by the transfer of an electron to cytochrome a are small, they may contribute to the regulation of the electron transfer by transient storage of the liberated energy as strain and atomic vibrations. Both the electron transfer and the conformational changes seem to be controlled by an attractor, i.e. by a manifestation of a deterministic chaos. The putative attractor is regular and is, for the reaction involving the inner monomer of ferricytochrome c (I), of the order of 3.03 +/- 0.03. The conformational changes involving the outer monomer of ferricytochrome c (O) seem also to be controlled by a regular attractor, but its order is 4.2 +/- 0.2. The low order of the coupled reactions of electron transfer and conformational change suggests that it is essential to the electron transfer process in the respiratory chain. Since the order of attractors of other proteins correlates with the vectorial description of the function (1.0 for myoglobin, 2.0 for chymotrypsin and lysozyme, 3.0 for an abenzyme), the value for cyt. c indicates that not only the electron transfer, but also an additional reaction, e.g. the conformational change, are essential for the function of this protein. Hence, the study of protein attractors may yield information on important details, which could not be obtained by other methods.

Animals↗
PubMed2005

Distinguishing random environmental fluctuations from ecological catastrophes for the North Pacific Ocean.

The prospect of rapid dynamic changes in the environment is a pressing concern that has profound management and public policy implications. Worries over sudden climate change and irreversible changes in ecosystems are rooted in the potential that nonlinear systems have for complex and 'pathological' behaviours. Nonlinear behaviours have been shown in model systems and in some natural systems, but their occurrence in large-scale marine environments remains controversial. Here we show that time series observations of key physical variables for the North Pacific Ocean that seem to show these behaviours are not deterministically nonlinear, and are best described as linear stochastic. In contrast, we find that time series for biological variables having similar properties exhibit a low-dimensional nonlinear signature. To our knowledge, this is the first direct test for nonlinearity in large-scale physical and biological data for the marine environment. These results address a continuing debate over the origin of rapid shifts in certain key marine observations as coming from essentially stochastic processes or from dominant nonlinear mechanisms. Our measurements suggest that large-scale marine ecosystems are dynamically nonlinear, and as such have the capacity for dramatic change in response to stochastic fluctuations in basin-scale physical states.

Animals↗
PubMed1980

Density-dependent selection in a random environment: An evolutionary process that can maintain stable population dynamics.

A theoretical analysis of natural selection is presented in which fitnesses depend on population density and randomly varying environmental processes. The theory is based on a general, heuristic analysis of a pair of coupled, nonlinear, stochastic difference equations that describe the joint dynamics of allele frequencies and population size. Four main conclusions emerge from the investigation of a particular class of models: (i) growth rates at low population densities tend to increase; (ii) individual selection, given sufficient genetic flexibility, will mold growth rates at higher densities so that in spite of i, stable deterministic population dynamics are maintained; (iii) "more fit" genotypes cannot be simply characterized-in particular, the mean population size need not be increased; and (iv) genetic polymorphisms can be maintained in both haploid and diploid organisms.

Journal Article↗
PubMed1999

Deterministic transport in ratchets.

We present the deterministic transport properties of driven overdamped particles in a simple piecewise-linear ratchet potential. We consider the effects on the stationary current due to local spatial asymmetry, time asymmetry in the driving force, and we include the possibility of a global spatial asymmetry. We present an extremely simple scheme for evaluating the current that is established on the ratchet within an "adiabatic" approximation, and compare the results with exact numerical integration of the process.

Journal Article↗
PubMed2001

Mean-field diffusion-limited aggregation: a "density" model for viscous fingering phenomena.

We explore a universal "density" formalism to describe nonequilibrium growth processes, specifically, the immiscible viscous fingering in Hele-Shaw cells (usually referred to as the Saffman-Taylor problem). For that we develop an alternative approach to the viscous fingering phenomena, whose basic concepts have been recently published in a Rapid Communication [Phys. Rev. E 63, 045305(R) (2001)]. This approach uses the diffusion-limited aggregation (DLA) paradigm as a core: we introduce a mean-field DLA generalization in stochastic and deterministic formulations. The stochastic model, a quasicontinuum DLA, simulates Monte Carlo patterns, which demonstrate a striking resemblance to natural Hele-Shaw fingers and, for steady-state growth regimes, follow precisely the Saffman-Taylor analytical solutions in channel and sector configurations. The relevant deterministic theory, a complete set of differential equations for a time development of density fields, is derived from that stochastic model. As a principal conclusion, we prove an asymptotic equivalency of both the stochastic and deterministic mean-field DLA formulations to the classic Saffman-Taylor hydrodynamics in terms of an interface evolution.

Journal Article↗
PubMed1988

Analytical review of structure and regulation of hemopoiesis.

Historical aspects of the accumulation of knowledge on the structure and kinetics of hemopoiesis are considered. Particular emphasis is placed upon kinetics of granulopoiesis based upon labeling of human granulocyte progenitors by tritiated thymidine (3HTdR) and the flow of labeled cells through mitosis and from a terminal mitosis through the non-dividing granulocytic pool into the blood. DNA synthesis time in myelocytes is 12-14 hours. The time from labeling of the myelocyte by 3HTdR to the appearance of labeled granulocytes in the blood is about 100 hours. Lobar pneumonia reduced the transit time from 100 to 48 hours in one patient. The deterministic model for granulopoiesis in human beings is described. Sterile inflammation and its effects on granulopoiesis was studied in the dog. Inflammation in tissue far from the bone marrow resulted in: 1. recruitment of a larger fraction of myelocytes into DNA synthesis; 2. increase in the rate of DNA synthesis in myelocytes; 3. increase in the number of mitoses in myelocytes; 4. increase in the rate of messenger transcription and translation so that a process involving synthesis of dozens of enzymes with their packaging into granules is shortened from 40 to 8 hours. It is likely that intramedullary production of GM-CSF and G-CSF are involved in the above processes. The nature of the chemical signal that mobilizes stored granulocytes from the marrow is not clear. Is there a factor produced in the inflammatory zone which circulates to the marrow and stimulates intramedullary production of GM-CSF and G-CSF? If so, are these the sole molecular regulators responsible for increasing the rate of granulopoiesis upon demand?

Animals↗
PubMed2005

Single-nucleosome mapping of histone modifications in S. cerevisiae.

Covalent modification of histone proteins plays a role in virtually every process on eukaryotic DNA, from transcription to DNA repair. Many different residues can be covalently modified, and it has been suggested that these modifications occur in a great number of independent, meaningful combinations. Published low-resolution microarray studies on the combinatorial complexity of histone modification patterns suffer from confounding effects caused by the averaging of modification levels over multiple nucleosomes. To overcome this problem, we used a high-resolution tiled microarray with single-nucleosome resolution to investigate the occurrence of combinations of 12 histone modifications on thousands of nucleosomes in actively growing S. cerevisiae. We found that histone modifications do not occur independently; there are roughly two groups of co-occurring modifications. One group of lysine acetylations shows a sharply defined domain of two hypo-acetylated nucleosomes, adjacent to the transcriptional start site, whose occurrence does not correlate with transcription levels. The other group consists of modifications occurring in gradients through the coding regions of genes in a pattern associated with transcription. We found no evidence for a deterministic code of many discrete states, but instead we saw blended, continuous patterns that distinguish nucleosomes at one location (e.g., promoter nucleosomes) from those at another location (e.g., over the 3' ends of coding regions). These results are consistent with the idea of a simple, redundant histone code, in which multiple modifications share the same role.

Chromatin Immunoprecipitation↗