The specificity of psychoanalytic concepts for understanding psychotherapy.
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Anxiety↗
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Results for “Probability Theory”
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Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?
The parametric description of residue environments through solvent accessibility, backbone conformation, or pairwise residue-residue distances is the key to the comparison between amino acid types at protein sequence positions and residue locations in structural templates (condition of protein sequence-structure match). For the first time, the research results presented in this study clarify and allow to quantify, on a rigorous statistical basis, to what extent the amino acid type-specific distributions of commonly used environment parameters are discriminative with respect to the 20 amino acid types. Relying on the Bahadur theory, we estimate the probability of error in a single-sequence-structure alignment based on weak or absent discriminative power in a learning database of protein structure. We present the results for many residue environment variables and demonstrate that each fold description parameter is sensitive with respect to only a few amino acid types while indifferent to most of the other amino acid types. Even complex structural characteristics combining solvent-accessible surface area, backbone conformation, and pairwise distances distinguish only some amino acid types, whereas the others remain nondiscriminated. We find that the knowledge-based potentials currently in use treat especially Ala, Asp, Gln, His, Ser, Thr, and Tyr as essentially "average" amino acids. Thus, highly discriminative amino acid types define the alignment register in gapless sequence-structure alignments. The introduction of gaps leads to alignment ambiguities at sequence positions occupied by nondiscriminated amino acid types. Therefore, local sequence-structure alignments produced by techniques with gaps cannot be reliable. Conceptionally new and more sensitive environment parameters must be invented.
Amino Acids↗
Combinatorial codons: a computer program to approximate amino acid probabilities with biased nucleotide usage.
Using techniques from optimization theory, we have developed a computer program that approximates a desired probability distribution for amino acids by imposing a probability distribution on the four nucleotides in each of the three codon positions. These base probabilities allow for the generation of biased codons for use in mutational studies and in the design of biologically encoded libraries. The dependencies between codons in the genetic code often makes the exact generation of the desired probability distribution for amino acids impossible. Compromises are often necessary. The program, therefore, not only solves for the "optimal" approximation to the desired distribution (where the definition of "optimal" is influenced by several types of parameters entered by the user), but also solves for a number of "sub-optimal" solutions that are classified into families of similar solutions. A representative of each family is presented to the program user, who can then choose the type of approximation that is best for the intended application. The Combinatorial Codons program is available for use over the web from http://www.wi.mit.edu/kim/computing.html.
Amino Acids↗
Sequence and temperature effect on hydrogen bond disruption in DNA determined by a statistical analysis.
We use the modified self-consistent phonon approximation theory to calculate temperature dependent interbase hydrogen bond disruption profiles for a number of six base pair repeating sequence infinite B-DNA polymers with various guanine-cytosine/adenine-thymine ratios. For comparison we also include results we have obtained in our earlier work on several B-DNA homopolymers, copolymers and a four-base-pair repeating sequence polymer. Our theory gives a statistical estimate of thermal fluctuational disruption probability of individual hydrogen bonds in individual base pairs in DNA as a function of temperature. The calculated probabilities show no sequence dependence at premelting temperatures, in agreement with proton exchange measurements. These probabilities however become very sensitive to base sequence at temperatures close to the observed melting temperatures. Multiphasic critical transitions are found in which a portion of base pairs are disrupted at temperature below the final disruption temperature. These transitions include localized as well as non-localized base pair opening. The localized transitions involve disruption of a few base-pairs at every other location without large scale base unstacking, and they may not appear in the observed UV curves with current resolution. On the other hand the overall disruption behavior is consistent with observations. The midpoint transition temperatures are close to the observed melting temperatures and these temperatures show the observed linear dependence on guanine-cytosine content. Our calculations indicate that our theory can be used effectively to calculate H-bond disruption behavior of different DNA sequences.
Base Sequence↗
Lévy laws in free probability.
This article and its sequel outline recent developments in the theory of infinite divisibility and Lévy processes in free probability, a subject area belonging to noncommutative (or quantum) probability. The present paper discusses the classes of infinitely divisible probability measures in classical and free probability, respectively, via a study of the Bercovici-Pata bijection between these classes.
Journal Article↗
Queuing theory under competitive social foraging may explain a mathematical equivalence of delay and probability in impulsive decision-making.
Intertemporal and probabilistic decision-making has been studied in psychiatry, ecology, and neuroeconomics. Because drug addicts and psycopaths often make risky decisions (e.g., drug misuse and aggression), investigation into types of impulsivity in intertemporal and probabilistic choices (delay and probability discounting) are important for psychiatric treatments. Studies in behavioral ecology proposed that delay and probability discounting are mediated by the same psychological process, because a decrease in probability of winning corresponds to an increase in delay until winning. According to this view, odds-against winning (=1/p-1) in probabilistic choice corresponds to delay in intertemporal choice. This hypothesis predicts that preference of gambling (low degree of probability discounting) may be associated with patience, rather than impulsivity or impatience, in intertemporal choice (low degree of delay discounting). However, recent empirical evidence in psychiatric research employing pathological gamblers indicates that pathological gamblers are impulsive in intertemporal choice (high degrees of delay discounting). However, a hyperbolic discounting function (usually adopted to explain intertemporal choice) with odds-against (instead of delay) explain experimental data in probabilistic choice dramatically well. Therefore, an alternative explanation is required for the hypothetical equivalence of odds-against to delay. We propose that queuing theory (often adopted for analyzing computer network traffic) under a competitive social foraging condition may explain the equivalence. Our hypothesis may help understand impulsivity of psychiatrics in social behavior (e.g., aggression and antisocial behavior) in addition to non-social impulsivity in reward-seeking (e.g., substance misuse).
Behavior, Addictive↗
The internal consistency of the standard gamble: tests after adjusting for prospect theory.
This article reports a study that tests whether the internal consistency of the standard gamble can be improved upon by incorporating loss weighting and probability transformation parameters in the standard gamble valuation procedure. Five alternatives to the standard EU formulation are considered: (1) probability transformation within an EU framework; and, within a prospect theory framework, (2) loss weighting and full probability transformation, (3) no loss weighting and full probability transformation, (4) loss weighting and no probability transformation, and (5) loss weighting and partial probability transformation. Of the five alternatives, only the prospect theory formulation with loss weighting and no probability transformation offers an improvement in internal consistency over the standard EU valuation procedure.
Adolescent↗
[Probability, truth and approximation of the truth. Epistemological criteria of preferability between theories; truth as a regulative ideal; and historical exemplification of progress in the knowledge of diabetes].
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Diabetes Mellitus↗
On the probability that a novel variant is a disease-causing mutation.
When a novel variant is found in a patient and not in a group of controls, it becomes a candidate for the disease-causing mutation in that patient. At present, no sampling theory exists for assessing the probability that the novel SNP might actually be a neutral variant. We have developed a population genetics-based method for calculating a P-value for a mutation-detection effort. Our method can be applied to a heterozygous patient, a homozygous patient, with or without inbreeding, or to a patient who is a compound heterozygote. Additionally, the method can be used to calculate the probability of finding a neutral variant at frequencies that differ between a group of patients and a group of controls, given some length of sequence examined. This method accounts for the multiple testing that is inherent in identification of variants through sequencing, to be used in subsequent case-control analyses. We show, for example, that for complete resequencing of 10 kb, the probability of finding a neutral variant in a patient and not in 50 controls is about 15%. Thus, discovery of a variant in a patient and not in a group of controls is, on its own, very weak evidence of involvement with disease.
Animals↗
Coping with novelty.
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Adaptation, Psychological↗
Symmetry broken motion of a periodically driven Brownian particle: nonadiabatic regime.
We report a theoretical study of an overdamped Brownian particle dynamics in the presence of both a spatially modulated one-dimensional periodic potential U(x) and a periodic alternating force (AF). As the periodic potential U(x) has a low symmetry (a ratchet potential) the Brownian particle displays a broken symmetry motion with a nonzero time average velocity. By making use of the Green function method and a mapping to the theory of Brillouin bands the probability distribution P(x,t) of the particle coordinate x is derived and the nonlinear dependence of the macroscopic velocity on the frequency omega and the amplitude eta of the AF is found. In particular, our theory allows to go beyond the adiabatic limit (omega=0) and to explain the peculiar reversal of the velocity sign found previously in the numerical analysis.
Journal Article↗
Signal probability effects on error detection performance in a quality control task.
This study was designed to examine the influence of signal probability on detection accuracy in a quality control task patterned after the checking of prescriptions in a pharmacy. Signal probability was defined as the ratio of erroneous scripts to correct scripts. 91 participants were either exposed to signal probabilities ranging from 26 to 30% ("low probability") or 34 to 38% ("high probability") while checking two sets of 40 simulated scripts for accuracy. Wrong item, wrong number, and wrong label information errors were possible, and performance was measured in terms of sensitivity (percentage of errors detected) and specificity (percentage of correct orders accepted). Analysis indicated that sensitivity was significantly worse for participants in the high signal probability condition, but specificity was not significantly different between signal probability conditions. Connections to existing theory and future directions for research are discussed.
Adult↗
Theory of interparticle correlations in dense, high-temperature plasmas. VI. Probability densities of the electric microfields.
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Journal Article↗
Typical versus atypical unpacking and superadditive probability judgment.
Probability judgments for packed descriptions of events (e.g., the probability that a businessman does business with a European country) are compared with judgments for unpacked descriptions of the same events (e.g., the probability that a businessman does business with England, France, or some other European country). The prediction that unpacking can decrease probability judgments, derived from the hypothesis that category descriptions are interpreted narrowly in terms of typical instances, is contrasted to the prediction of support theory that unpacking will generally increase judged probabilities (A. Tversky & D. J. Koehler, 1994). The authors varied the typicality of unpacked instances and found no effect of unpacking with typical instances (additivity) and a negative effect with atypical instances (superadditivity). Support theory cannot account for these findings in its current formulation.
Humans↗
A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate.
Under prevailing theories, the nonsynonymous-to-synonymous substitution ratio (i.e. K(a)/K(s)), which measures the fixation probability of nonsynonymous mutations, is correlated with the strength of selection. In this article, we report that K(a)/K(s) is also strongly correlated with the mutation rate as measured by K(s), and that this correlation appears to have a similar magnitude as the correlation between K(a)/K(s) and selective strength. This finding cannot be reconciled with current theories. It suggests that we should re-evaluate the current paradigms of coding-sequence evolution, and that the wide use of K(a)/K(s) as a measure of selective strength needs reassessment.
Animals↗
Attentional bias between modalities: effect on the internal clock, memory, and decision stages used in animal time discrimination.
Both the presentation of unbalanced stimulus probabilities and the insertion of a predictive cue prior to the signal on each trial apparently induces a strong bias to use a particular stimulus modality in order to select a temporal criterion and response rule. This attentional bias toward one modality is apparently independent of the modality of the stimulus being timed and is strongly influenced by stimulus probabilities or prior warning cues. These techniques may be useful to control trial-by-trial sequential effects that influence a subject's perceptual and response biases when signals from more than one modality are used in duration discrimination tasks. Cross-procedural generality of the effects of attentional bias was observed. An asymmetrical modality effect on the latency to begin timing was observed with both the temporal bisection and the peak procedure. The latency to begin timing light signals, but not the latency to begin timing sound signals, was increased when the signal modality was unexpected. This asymmetrical effect was explained with the assumption that sound signals close the mode switch automatically, but that light signals close the mode switch only if attention is directed to the light. The time required to switch attention is reflected in a reduction of the number of pulses from the pacemaker that enter the accumulator. One positive aspect of this work is the demonstration that procedures similar to those used to study human cognition can be used with animal subjects with similar results. Perhaps these similarities will stimulate animal research on the physiological basis of various cognitive capacities. Animal subjects would be preferred for such physiological experimentation if it were established that they possessed some of the cognitive processes described by investigators of human information processing. One of the negative aspects of this work is that only one combination of modalities was used and variables such as stimulus intensity, stimulus probability, and range of signal durations have not been adequately investigated at present. Future work might test additional combinations of modalities and vary stimulus intensity and stimulus probability within a signal detection theory (SDT) framework to determine the effects of these variables on attentional bias.
Animals↗
[The biology of depression].
There are several arguments in favor of a biological cause of endogenous depressions coming from clinical experience, genetic studies and the pharmacology of antidepressants. Impaired impulse transmission across the synapses of noradrenergic and serotoninergic systems has been for 20 years considered to be the underlying defect. In contrast to earlier theories this defect consists more probably in an altered sensitivity of post-synaptic receptors than in reduced concentration of the amines. As neurotransmission is regulated in a complex way the interpretation of experimental results is often ambiguous. The noradrenergic medial forebrain bundle, part of the reward system, is of special importance for a biological theory of depression.
Antidepressive Agents↗
Continuous probability distributions from finite data.
Recent approaches to the problem of inferring a continuous probability distribution from a finite set of data have used a scalar field theory for the form of the prior probability distribution. This paper presents a more general form for the prior distribution that has a geometrical interpretation and can improve the specificity of likely solutions. It is also demonstrated that a numerical sampling of the posterior probability distribution can be used as an alternative to a histogram for visualization and to make probabilistic inferences from the data.
Fourier Analysis↗