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At least 649 records · Page 36Linked to original sources
PubMed2005

Electron tunneling of photochemical reactions on metal surfaces: nonequilibrium Green's function-density functional theory approach to photon energy dependence of reaction probability.

We have developed a theoretical model of photoinduced reactions on metal surfaces initiated by the substrate/indirect excitation mechanism using the nonequilibrium Green's function approach. We focus on electron transfer, which consists of (1) electron-hole pair creation, (2) transport of created hot electrons, and (3) tunneling of hot electrons to form an anion resonance. We assume that steps (1), (2), and (3) are separable. By this assumption, the electron dynamics might be restated as a tunneling problem of an open system. Combining the Keldysh time-independent formalism with the simple transport theory introduced by Berglund and Spicer, we present a practical scheme for first-principle calculation of the reaction probability as a function of incident photon energy. The method is illustrated by application to the photoinduced desorption/dissociation of O2 on a Ag(110) surface by adopting density functional theory.

Journal Article↗
PubMed2002

Using imprecise probabilities to address the questions of inference and decision in randomized clinical trials.

Randomized controlled clinical trials play an important role in the development of new medical therapies. There is, however, an ethical issue surrounding the use of randomized treatment allocation when the patient is suffering from a life threatening condition and requires immediate treatment. Such patients can only benefit from the treatment they actually receive and not from the alternative therapy, even if it ultimately proves to be superior. We discuss a novel new way to analyse data from such clinical trials based on the use of the recently developed theory of imprecise probabilities. This work draws an explicit distinction between the related but nevertheless distinct questions of inference and decision in clinical trials. The traditional question of scientific interest asks 'Which treatment offers the greater chance of success?' and is the primary reason for conducting the clinical trial. The question of decision concerns the welfare of the patients in the clinical trial, asking whether the accumulated evidence favours one treatment over the other to such an extent that the next patient should decline randomization and instead express a preference for one treatment. Consideration of the decision question within the framework of imprecise probabilities leads to a mathematical definition of equipoise and a method for governing the randomization protocol of a clinical trial. This paper describes in detail the protocol for the conduct of clinical trials based on this new method of analysis, which is illustrated in a retrospective analysis of data from a clinical trial comparing the anti-emetic drugs ondansetron and droperidol in the treatment of postoperative nausea and vomiting. The proposed methodology is compared quantitatively using computer simulation studies with conventional clinical trial designs and is shown to maintain high statistical power with reduced sample sizes, at the expense of a high type I error rate that we argue is irrelevant in some specific circumstances. Particular emphasis is placed on describing the type of medical conditions and treatment comparisons where the new methodology is expected to provide the greatest benefit.

Antiemetics↗
PubMed1989

A patient with new Q waves: methods for decision making in the individual patient.

Decision analysis, an analytic approach to making decisions when uncertainty is present, has its foundation in probability and utility theory. It provides insights into the trade-offs that are involved when a selection must be made among patient management strategies. In general, several broad steps are involved. The process begins by formulating the clinical problem as a well focused choice among a limited set of clinical etiologies. These strategies are then structured explicitly in a model that depicts the clinical events that may ensue from each option. By assigning probability values to each outcome, the weighted average outcome or expected utility can be calculated for each alternative strategy. The strategy with the highest expected utility is the optimal one. The methods of decision analysis offer a number of distinct advantages. These include: 1) providing a structure with which to simplify and focus clinical dilemmas; 2) providing a forum for discussing clinical reasoning; and 3) developing a consensus among groups of decision makers.

Aged↗
PubMed1995

A theory of tension fluctuations due to muscle cross-bridges.

We present an analytical theory for the spectrum of tension fluctuations due to muscle cross-bridges. The theory is based upon the Langevin theory of brownian motion, and is illustrated using a simplified three-state model for the cross-bridge cycle, which is intended to model cross-bridges in fibrillar insect flight muscle. Langevin white-noise sources, representing fluctuations in the net transition rates for each step in the cycle, are introduced into the rate equations, and their strengths are adjusted to give the correct mean-square fluctuations in the occupation probabilities. The Langevin theory shows that the noise is closely related to the elastic properties of cross-bridges, and it also shows in detail how each step in the cross-bridge cycle contributes differently to the noise spectrum. We find that the total noise increases with filament displacement. For small filament displacements, the noise is dominated by the power stroke and by dissociation at the end of the cycle. These contributions increase in the region of stretch activation, whilst at larger displacements, where the cross-bridge becomes locked in the strong-binding state, the noise is much larger and is dominated by attachment and detachment at the beginning of the cycle. The cross-bridge properties in this regime are strongly affected by free inorganic phosphate. Finally, we show how the noise spectrum is modified by the inclusion of a series compliance representing a practical force transducer.

Animals↗
PubMedDate not supplied

[The theory of functional systems and probabilistic prognosis of behavior].

The article is dedicated to possible probability prediction of behavior in system organization of behavioral acts. System mechanisms of anticipation of required results of behavioral activity by living organisms adapted to stable and changing conditions of life are discussed. The author proposes that in all forms of behavior, an organism strictly predicts parameters for satisfaction of dominating needs of results that constitute the goal of a given form of behavior. In author's opinion, the probabilistic prognosis concerns only methods, acts and attendant emotional states, as well as possible ways of attaining the results (i.e., the means rather than action parameters).

Affect↗
PubMed2004

Bayes and health care research.

Bayes' rule shows how one might rationally change one's beliefs in the light of evidence. It is the foundation of a statistical method called Bayesianism. In health care research, Bayesianism has its advocates but the dominant statistical method is frequentism. There are at least two important philosophical differences between these methods. First, Bayesianism takes a subjectivist view of probability (i.e. that probability scores are statements of subjective belief, not objective fact) whilst frequentism takes an objectivist view. Second, Bayesianism is explicitly inductive (i.e. it shows how we may induce views about the world based on partial data from it) whereas frequentism is at least compatible with non-inductive views of scientific method, particularly the critical realism of Popper. Popper and others detail significant problems with induction. Frequentism's apparent ability to avoid these, plus its ability to give a seemingly more scientific and objective take on probability, lies behind its philosophical appeal to health care researchers. However, there are also significant problems with frequentism, particularly its inability to assign probability scores to single events. Popper thus proposed an alternative objectivist view of probability, called propensity theory, which he allies to a theory of corroboration; but this too has significant problems, in particular, it may not successfully avoid induction. If this is so then Bayesianism might be philosophically the strongest of the statistical approaches. The article sets out a number of its philosophical and methodological attractions. Finally, it outlines a way in which critical realism and Bayesianism might work together.

Bayes Theorem↗
PubMed1989

Psychometric functions for the discrimination of differences in intensity of Gaussian noise.

A new theory of sensory functioning by Laming predicts how the shape of the psychometric function depends on the context in which a signal is presented. The discrimination of intensities of noise was therefore studied with four different stimulus configurations. In one, observers discriminated between two separate noise samples that differed in intensity. In accordance with the theory, a normal probability integral provided a better fit to each observer's data than either of two other functions: a normal integral with respect to the square of the difference, or a normal integral with respect to the fourth power of the difference. In a second task, observers detected an increment in a continuous noise. For eight out of nine sets of data, a square-law function provided a better fit than either a normal integral or fourth-power function. A third task asked observers to decide which of two noises was amplitude modulated. The predicted square-law function provided the best fit for four out of five observers. In a fourth task, one observer detected an interval of amplitude modulation in a continuous noise. As predicted by the theory, a fourth-power function provided the best fit. In addition, Weber fractions for difference discriminations decreased approximately with the square root of sample duration for durations up to 300 msec, whereas Weber fractions for increment detections decreased approximately directly with duration for durations up to 100 msec. The results are usually in qualitative agreement with the theory and often in quantitative agreement as well.

Adult↗
PubMed2004

Practical introduction to record linkage for injury research.

The frequency of early fatality and the transient nature of emergency medical care mean that a single database will rarely suffice for population based injury research. Linking records from multiple data sources is therefore a promising method for injury surveillance or trauma system evaluation. The purpose of this article is to review the historical development of record linkage, provide a basic mathematical foundation, discuss some practical issues, and consider some ethical concerns. Clerical or computer assisted deterministic record linkage methods may suffice for some applications, but probabilistic methods are particularly useful for larger studies. The probabilistic method attempts to simulate human reasoning by comparing each of several elements from the two records. The basic mathematical specifications are derived algebraically from fundamental concepts of probability, although the theory can be extended to include more advanced mathematics. Probabilistic, deterministic, and clerical techniques may be combined in different ways depending upon the goal of the record linkage project. If a population parameter is being estimated for a purely statistical study, a completely probabilistic approach may be most efficient; for other applications, where the purpose is to make inferences about specific individuals based upon their data contained in two or more files, the need for a high positive predictive value would favor a deterministic method or a probabilistic method with careful clerical review. Whatever techniques are used, researchers must realize that the combination of data sources entails additional ethical obligations beyond the use of each source alone.

Databases, Factual↗
PubMed1992

A theoretical basis for conditional probability analyses of neural discharge activity.

A theory has been developed which allows the estimation of the probability density of a discharge, given that an arbitrary condition is fulfilled. It is shown that the common methods for the evaluation of a post-stimulus time (PST) histogram and a hazard function can be considered as special applications of this theory. Whereas the usual hazard function shows how the probability of a discharge depends on the time elapsed since the last discharge, generalized hazard functions proposed in the present paper allow to reveal also the influence of the last but one discharge, the last but two discharge, and so on. In contrast to the usual method for the estimation of a hazard function, the applicability of the procedures proposed here is not restricted to stationary discharge activity. Some elementary applications are illustrated by analysing simulated discharge activity mimicing the response of a single auditory-nerve fiber to a high-intensity tone burst.

Action Potentials↗
PubMed1975

The effect of signal probability, food intake, sex, and smoking on gustation, as measured by the theory of signal detection.

The possibility of applying Signal Detection Theory (SDT) to gustation was investigated by testing the effect of three variables--smoking, signal probability, and food intake (confounded with time of day)--on the taste sensitivity to sucrose of 24 male and 24 female Ss. No main effects or interactions were significant. The study indicated a "warm-up" effect, while adaptation was questionable. An analysis of false alarm (FA) reports was undertaken and discussed. Correlations were obtained between numerous variables and sensitivity. None of the correlations was statistically significant. It was concluded that although SDT is theoretically applicable to the gustatory modality, it is not practical for large-scale research.

Differential Threshold↗
PubMed1984

Diagnostic efficiency and DSM-III.

This study critiques and extends the DSM-III use of fixed and explicit criteria by applying principles and statistics common within actuarial decision theory (eg, conditional probabilities). The value and limitations of sensitivity and specificity rates are discussed and compared with an interesting but rarely used statistic, positive predictive power. The statistics and analyses provided herein also provide an empirical method for developing diagnostic criteria and determining when and how the DSM-III cutoff points might be adjusted, recognize the importance of base rates and utilities to efficient diagnosis, and provide an explicit, quantitative means by which to make optimal differential diagnoses and to make use of the overlap among psychiatric diagnoses. The issues are illustrated in the differential diagnosis of the Borderline Personality Disorder, but they have a relevance to the development and application of the other DSM-III diagnoses.

Borderline Personality Disorder↗
PubMed1995

Statistical issues in DNA evidence.

Some of the statistical issues involved in the interpretation of DNA evidence in courts, particularly focusing on the adversarial process as seen in the UK and the USA, are discussed. The appropriate way to consider the use of DNA evidence in courts is through the use of a likelihood ratio. In this, the relative likelihoods of the DNA evidence are calculated under two hypotheses, respectively that the subject is or is not the source of a DNA sample found at the scene-of-crime. This formulation allows, using Bayes' theory, the prior probability of guilt, based on the other evidence in a case, to be incorporated in a formal way into calculation of a final, or posterior, probability of guilt. The most controversial aspect of DNA evidence has concerned the calculation of the probability of a match between an innocent suspect and DNA from the scene-of-crime. The calculation is affected by subdivision within the population and the possibility of relatedness between the suspect and the true source of the scene-of-crime DNA. The qualitative importance of these effects will be discussed. In addition to the scientific questions concerning the likelihood ratio, there have been a number of other concerns about the use of DNA evidence, and other evidence presented in a statistical form, in courts. These include the question whether accurate or conservative values of the likelihood ratio should be presented, and the abilities of juries to deal with quantitative evidence.

DNA↗
PubMed2006

QBES: predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization.

Solvent accessibility, one of the key properties of amino acid residues in proteins, can be used to assist protein structure prediction. Various approaches such as neural network, support vector machines, probability profiles, information theory, Bayesian theory, logistic function, and multiple linear regression have been developed for solvent accessibility prediction. In this article, a much simpler quadratic programming method based on the buriability parameter set of amino acid residues is developed. The new method, called QBES (Quadratic programming and Buriability Energy function for Solvent accessibility prediction), is reasonably accurate for predicting the real value of solvent accessibility. By using a dataset of 30 proteins to optimize three parameters, the average correlation coefficients between the predicted and actual solvent accessibility are about 0.5 for all four independent test sets ranging from 126 to 513 proteins. The method is efficient. It takes only 20 min for a regular PC to obtain results of 30 proteins with an average length of 263 amino acids. Although the proposed method is less accurate than a few more sophisticated methods based on neural network or support vector machines, this is the first attempt to predict solvent accessibility by energy optimization with constraints. Possible improvements and other applications of the method are discussed.

Protein Conformation↗
PubMed1978

The clearing of excess potassium from extracellular space in spinal cord and cerebral cortex.

The relative importance of active and passive transport processes in the clearing of potassium released from active neurons was estimated Extracellular potassium activity [K+]0 was measured with ion-selective microelectrodes in the sensory area of the neocortex and in lumbosacral spinal cord of cats. Transient elevation of [K+]0 was evoked in cortex by stimulation of VPL and in spinal cord by stimulation of afferent nerves. The rate with which excess [K+]0 was cleared was either feebly or not at all influenced by variation of the intensity and frequency of stimulation. The half-decay times of [K+]0 were however prolonged when the duration of stimulus trains was increased. Only small differences were seen in the rate of decay of [K+]0 transients recorded at different locations within the gray matter; the shortest half-decay times occurred where K+ responses were largest. The different profiles of distribution of delta [K+]0 in response to stimulation of the cortical surface and of VPL nucleus were mapped. As in spinal cord also in cortex the distribution of the evoked sustained shifts of electric potential mirrored the distribution of [K+]0 transients. The rate at which K+ could diffuse out of volume sources similar in magnitude to the volumes of distribution of [K+]0 responses in gray matter were calculated. The observed half-decay times of [K+]0 transients were more than a hundred times shorter than those calculated for diffusion either in spinal cord or in cortex. Intravenous administration of digitoxigenin was shown to retard the clearing of [K+]0 and caused an elevation of the unstimulated [K+]0 baseline. Seizures were frequently induced by digitoxigenin when the [K+]0 baseline was only slightly elevated, and the occurrence of seizures was not associated with a definable threshold level of [K+]0. It is concluded that active reuptake is the principal mechanism of the clearing of [K+]0 released by neurons. Redistribution of K+ by diffusion must have been negligible under the conditions of these experiments, but may be more important when only a few neurons release K+ amongst many inactive cells. Considerations of a glial transport network are probably inconsequential for theories of the generation of seizures.

Afferent Pathways↗
PubMed1985

The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation.

A quantitative model has been developed for processes in the bacteriophage lambda that control the switchover from lysogenic to lytic modes of growth. These processes include the interactions of cI repressor and cro proteins at the three DNA sites of the right operator, OR, the binding of RNA polymerase at promoters PR and PRM, the synthesis of cI repressor and cro proteins, and the degradative action of recA during induction of lysis. The model is comprised of two major physical-chemical components: a statistical thermodynamic theory for relative probabilities of the various molecular configurations of the control system; and a kinetic model for the coupling of these probabilities to functional events, including synthesis of regulatory proteins cI and cro. Using independently evaluated interaction constants and rate parameters, the model was found capable of predicting essential physiological characteristics of the system over an extended time. Sufficiency of the model to predict known physiological properties lends credence to the physical-chemical assumptions used in its construction. Several major physiological characteristics were found to arise as "system properties" through the non-linear, time-dependent, feedback-modulated combinations of molecular interactions prescribed by the model. These include: maintenance of the lysogenic state in the absence of recA-mediated cI repressor degradation; induction of lysis and the phenomenon of subinduction; and autogenous negative control of cro. We have used the model to determine the roles, within the composite system, of several key molecular processes previously characterized by studies in vitro. These include: co-operativity in cI repressor binding to DNA; interactions between repressors and RNA polymerase (positive control); and the monomer-dimer association of cI repressor molecules. A major role of cI repressor co-operativity is found to be that of guaranteeing stability of the lysogenic state against minor changes in cI repressor levels within the cell. The role of positive control seems to be that of providing for a peaked, rather than monotonic, dependence of PRM activity on cI repressor level, while permitting PR activity to be a step function. The model correlates an immense body of studies in vivo and in vitro, and it makes testable predictions about molecular phenomena as well as physiological characteristics of bacteriophage lambda. The approach developed in this study can be extended to include more features of the lambda system and to treat other systems of gene regulation.

Allosteric Regulation↗
PubMed1985

Analysis and optimization of recombinant DNA joining reactions.

The statistical segment length of duplex DNA was determined in phage T4 ligase (poly(deoxyribonucleotide): poly(deoxyribonucleotide) ligase (AMP forming), EC 6.5.1.1) buffer (50 mM-Tris . HCl (pH 7.8), 20 mM-dithiothreitol, 10 mM-MgCl2, 1 mM-ATP) at 12 degrees C to be 1030(+/- 116) A. This result was obtained by electron microscopic examination of the molecular distributions generated by T4 ligase-mediated joining of EcoRI-cleaved pBR322 DNA. This value of the statistical segment length was utilized in an extension of the Jacobson-Stockmayer theory on the probability of intramolecular cyclization in order to optimize DNA joining reactions that are of great utility in recombinant DNA experiments. Five cloning systems were analyzed: circular plasmid vectors that had been linearized with one or two restriction endonucleases, circular plasmids that had been tailed with deoxyhomopolymers before joining, lambda-type cloning vectors and cosmids. The results are tabulated for convenient use in molecular cloning experiments.

Cloning, Molecular↗
PubMed2006

The role of variance in capped-rate stochastic growth models with external mortality.

Techniques from queueing theory can be used to model the growth of individuals in a stochastic environment where the growth rate cannot exceed some physiological maximum. In the simplifying case where there are no metabolic costs and the individual has an unlimited gut size, a general theory for the probability of reaching a target weight is presented. The role of environmental variance is examined in two different cases; randomly varying prey size and clustering in the prey arrival rate. It is argued that when food is scarce environmental stochasticity is beneficial to the individual but when food is abundant it can lower the chance of survival. The growth and recruitment of larval fish is used as an example.

Animals↗
PubMedDate not supplied

Making sense of sparse rating data in collaborative filtering via topographic organization of user preference patterns.

We introduce topographic versions of two latent class models (LCM) for collaborative filtering. Latent classes are topologically organized on a square grid. Topographic organization of latent classes makes orientation in rating/preference patterns captured by the latent classes easier and more systematic. The variation in film rating patterns is modelled by multinomial and binomial distributions with varying independence assumptions. In the first stage of topographic LCM construction, self-organizing maps with neural field organized according to the LCM topology are employed. We apply our system to a large collection of user ratings for films. The system can provide useful visualization plots unveiling user preference patterns buried in the data, without loosing potential to be a good recommender model. It appears that multinomial distribution is most adequate if the model is regularized by tight grid topologies. Since we deal with probabilistic models of the data, we can readily use tools from probability and information theories to interpret and visualize information extracted by our system.

Behavior↗