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Learning new words: phonotactic probability in language development.

Though the influences of syntactic and semantic regularity on novel word learning are well documented, considerably less is known about the influence of phonological regularities on lexical acquisition. The influence of phonotactic probability, a measure of the likelihood of occurrence of a sound sequence, on novel word learning is investigated in this study. Thirty-four typically developing children (from ages 3 years 2 months to 6 years 3 months) participated in a multitrial word-learning task involving nonwords of varying phonotactic probability (common vs. rare) paired with unfamiliar object referents. Form and referent learning were tested following increasing numbers of exposures (1 vs. 4 vs. 7) and following a 1-week delay. Correct responses were analyzed to determine whether phonotactic probability affected rate of word learning, and incorrect responses were analyzed to examine whether phonotactic probability affected the formation of semantic representations, lexical representations, or the association between semantic and lexical representations. Results indicated that common sound sequences were learned more rapidly than rare sound sequences across form and referent learning. In addition, phonotactic probability appeared to influence the formation of semantic representations and the association between semantic and lexical representations. These results are integrated with previous findings and theoretical models of language acquisition.

Child↗

Methods for minimizing the confounding effects of word length in the analysis of phonotactic probability and neighborhood density.

Recent research suggests that phonotactic probability (the likelihood of occurrence of a sound sequence) and neighborhood density (the number of words phonologically similar to a given word) influence spoken language processing and acquisition across the lifespan in both normal and clinical populations. The majority of research in this area has tended to focus on controlled laboratory studies rather than naturalistic data such as spontaneous speech samples or elicited probes. One difficulty in applying current measures of phonotactic probability and neighborhood density to more naturalistic samples is the significant correlation between these variables and word length. This study examines several alternative transformations of phonotactic probability and neighborhood density as a means of reducing or eliminating this correlation with word length. Computational analyses of the words in a large database and reanalysis of archival data supported the use of z scores for the analysis of phonotactic probability as a continuous variable and the use of median transformation scores for the analysis of phonotactic probability as a dichotomous variable. Neighborhood density results were less clear with the conclusion that analysis of neighborhood density as a continuous variable warrants further investigation to differentiate the utility of z scores in comparison to median transformation scores. Furthermore, balanced dichotomous coding of neighborhood density was difficult to achieve, suggesting that analysis of neighborhood density as a dichotomous variable should be approached with caution. Recommendations for future application and analyses are discussed.

Adult↗

The effect of qualitative vs. quantitative presentation of probability estimates on patient decision-making: a randomized trial.

BACKGROUND: Given the greater uncertainty surrounding probability estimates associated with qualitative (use of words or phrases) descriptions, the use of quantitative (numerical) information to communicate the risks and benefits of therapies is recommended but the impact of its use in decision aids is unexplored. OBJECTIVE: Using stroke prevention in atrial fibrillation as an example, to compare the impact of quantitative vs. qualitative descriptions of probability risk estimates in decision aids on the clinical decision-making process. DESIGN: Randomized trial with a 2 x 2 factorial design. SUBJECTS: A total of 198 volunteers aged 60-80 years. SETTING: Outpatient clinics of a university-affiliated, tertiary-care teaching hospital. METHODS: Participants were asked to imagine that they had atrial fibrillation, and using a decision aid, were then randomized to two ways of receiving pertinent risk information regarding the probability of stroke and major bleeding when taking warfarin, aspirin or no therapy: (1) quantitatively, in which the 2-year probabilities of stroke and major haemorrhage were presented both numerically and graphically with 100 faces (e.g. 8 of 100), and (2) qualitatively in which these probabilities were presented with the use of verbal phrases (e.g. very low, moderate). OUTCOME MEASURES: Primary: decisional conflict. Secondary: participants' choices, knowledge and expectations of outcomes using qualitative and quantitative scales. RESULTS: Participants reviewing quantitative risk information scored better on the informed subscale of the decisional conflict scale (P < 0.05) and, as expected, were better able to estimate numerically their chance of stroke and bleeding when taking warfarin, aspirin or no medication. For the low risk arm, there were no significant differences in treatment choices for the qualitative and quantitative groups. For the moderate risk arm, treatment choices between the two groups were significantly different (P = 0.01), with those in the quantitative group more likely to make an actual choice and to choose therapies at the extremes of effectiveness (warfarin and no treatment). There were no significant differences between the quantitative and qualitative groups in their ability to rank-order their stroke risk when taking warfarin, aspirin and no treatment, overall knowledge about atrial fibrillation and its treatment, and other dimensions of decisional conflict (all P-values >0.05). CONCLUSIONS: For participants without the disease in question, this study found that providing sufficient quantitative risk information makes them feel more informed, which sometimes affects their treatment choices. Further studies are necessary to confirm these findings for patients making actual clinical decisions.

Aged↗

A probability model for predicting BRCA1 and BRCA2 mutations in breast and breast-ovarian cancer families.

Germline mutations in BRCA1 and BRCA2 genes predispose to hereditary breast and ovarian cancer. Our aim was to find associations between the clinical characteristics and positive mutation status in 148 breast cancer families in order to predict the probability of finding a BRCA mutation in a family. Several factors were associated with mutations in univariate analysis, whereas in multivariate analysis (logistic regression with backward selection) only the age of the youngest breast cancer patient and the number of ovarian cancer cases in a family were independent predictors of BRCA mutations. A logistic model was devised to estimate the probability for a family of harbouring a mutation in either BRCA1 or BRCA2. Altogether, 63 out of 148 families (43%) and 28 out of 29 (97%) mutation carrier families obtained probabilities over 10%. The mean probability was 55% for mutation-positive families and 11% for mutation-negative families. The models by Couch et al (1997) and Shattuck-Eidens et al (1997) previously designed for BRCA1 were also tested for their applicability to distinguish carrier families with mutations in either gene. The probability model should be a useful tool in genetic counselling and focusing the mutation analyses, and thus increasing also the cost-effectiveness of the genetic screening.

Adult↗

The influence of the probability of survival on patients' preferences regarding cardiopulmonary resuscitation.

BACKGROUND: Studies suggest that a majority of elderly patients would want to undergo cardiopulmonary resuscitation (CPR) if they had a cardiac arrest. Yet few studies have examined their preferences after clinicians have informed them about the outcomes of CPR. METHODS: To study older patients' preferences regarding CPR, we interviewed as many ambulatory patients as possible in one geriatrics practice in Denver from August 1, 1991, through July 31, 1992. RESULTS: A total of 371 patients at least 60 years of age were eligible; 287 completed the interview (mean age, 77 years; range, 60 to 99). When asked about their wishes if they had cardiac arrest during an acute illness, 41 percent opted for CPR before learning the probability of survival to discharge. After learning the probability of survival (10 to 17 percent), 22 percent opted for CPR. Only 6 percent of patients 86 years of age or older opted for CPR under these conditions. When asked about a chronic illness in which the life expectancy was less than one year, 11 percent of the 287 patients opted for CPR before learning the probability of survival to discharge. After learning the probability of survival (0 to 5 percent), 5 percent said they would want CPR. CONCLUSIONS: Older patients readily understand prognostic information, which influences their preferences with respect to CPR. Most do not want to undergo CPR once a clinician explains the probability of survival after the procedure.

Advance Directives↗

Low Ba2+ and Ca2+ induce a sustained high probability of repolarization openings of L-type Ca2+ channels in hippocampal neurons: physiological implications.

Openings of single L-type Ca2+ channels following repolarization to negative membrane potentials from a depolarizing step (repolarization openings, ROs) have been described previously in brain cell preparations. However, these ROs have been reported to occur only infrequently. Here we report that the frequency of ROs in cell-attached patches of cultured rat hippocampal neurons can be increased dramatically by lowering the pipette Ba2+ concentration to 20 mM from the usual 90-110 mM. This increased opening probability can last for hundreds to thousands of milliseconds following repolarization. Current-voltage analyses of open probability show that the depolarization pulse threshold for inducing ROs in 20 mM Ba2+ is -10 to 0 mV but that the probability of ROs reaches maximal levels following depolarizing pulses that approach the apparent null (equilibrium) potential for Ba2+. Comparable current-voltage curves in 110 mM Ba2+ from a more positive holding potential (-50 mV) indicate that membrane surface charge screening accounts for some, but not all, of the effect of lowering the Ba2+ concentration. Consequently, current-dependent inactivation or some other ion-dependent mechanism (e.g., ion binding inside the pore) also appears to regulate this potentially major pathway of Ca2+ entry. A high probability of ROs also can be induced under relatively physiological conditions (5-ms depolarizing steps, 2-5 mM Ca2+ in the pipette). Thus, the high open probability state at negative potentials may underlie the long Ca2+ tail currents in hippocampus that were described previously and appears to have major implications for physiological functions (e.g., the slow Ca(2+)-dependent afterhyperpolarization), particularly in brain neurons.

3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethy↗

Decision making in sport: the effect of stimulus-response probability on the performance of a coincidence-anticipation task.

The purpose of the present study was to evaluate the quality of a motor response for different levels of expectancy and time constraint, in a two-choice coincidence-anticipation task. The probability of each of the two events likely to be presented were varied across different levels as well as the speed of the stimulus to be intercepted. The results indicated that neither the choice reaction time (CRT) and movement time, nor the performance of coincidence-anticipation were affected by the probability of the stimulus for the low and moderate stimulus speeds. However, when the stimulus traveled at a high speed a trade-off took place. The CRT decreased as the probability of the event increased, whilst the proportion of response initiation errors increased for the low probability events. This trade-off resulted in a better coincidence-anticipation as the probability of the event increased. The results obtained in the present experiment are clearly different from those obtained in a classic CRT-deadline paradigm, in that the trade-off observed between CRT and response initiation errors was far less pronounced in the coincidence-anticipation task. This difference was attributed to the higher negative consequences associated with a response initiation error in a coincidence-anticipation task. It is thus concluded that the tasks used to study the nature of the decision processes taking place in sports and sports-like situations must have some ecological validity to be of some help for the practitioner.

Adult↗

Probability lower bounds for USP/NF tests.

In the pharmaceutical industry, a number of tests such as content uniformity and dissolution testing are usually performed at various stages of drug manufacturing process to ensure that the drug product meets standards for identity, strength, quality, purity, and stability of the drug product as specified in the United States Pharmacopedia and National Formulary (USP/NF). The USP/NF provides requirements for sampling plans, testing procedures, and acceptance criteria for these tests. To ensure that there is a high probability of passing the USP/NF tests, the sponsors usually establish in-house specification limits based on some lower bounds of the probabilities of passing USP/NF tests for future samples. In this article, we derive some probability lower bounds for USP/NF tests. It is shown that the proposed probability lower bounds are better than the existing ones and are very close to the true probabilities in a broad range of the population mean and variance of the test sample.

Drug Compounding↗

Using substitution matrices to estimate probability distributions for biological sequences.

Accurately estimating probabilities from observations is important for probabilistic-based approaches to problems in computational biology. In this paper we present a biologically-motivated method for estimating probability distributions over discrete alphabets from observations using a mixture model of common ancestors. The method is an extension of substitution matrix-based probability estimation methods. In contrast to previous such methods, our method has a simple Bayesian interpretation and has the advantage over Dirichlet mixtures that it is both effective and simple to compute for large alphabets. The method is applied to estimate amino acid probabilities based on observed counts in an alignment and is shown to perform comparably to previous methods. The method is also applied to estimate probability distributions over protein families and improves protein classification accuracy.

Amino Acid Sequence↗

Base pairing probabilities in a complete HIV-1 RNA.

We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill (1990). By analyzing the full distribution of base pair probabilities instead of a restricted number of secondary structures, we gain more complete and reliable information about the secondary structure of HIV-1. We introduce methods that condense the information in the probability distribution to one value per nucleotide in the sequence. Using these methods we represent the secondary structure as a weighted average of the base pair probabilities, and we can identify interesting secondary structures that have relatively well-defined base pairing. The results show high probabilities for the known secondary structures at the 5'-end of the molecule that have been predicted on the basis of biochemical data. The Rev response element (RRE) appears as a distinct element in the secondary structure. It has a meta-stable domain at the high affinity site for the binding of Rev. The overall structure decomposes into fairly small independent structures in the first 4,000 bases of the molecule. The remaining 5,000 bases (excluding the terminal repeat) form a single, large structure, on top of which the RRE is located.

Algorithms↗

Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences.

Accurately estimating probabilities from observations is important for probabilistic-based approaches to problems in computational biology. In this paper we present a biologically-motivated method for estimating probability distributions over discrete alphabets from observations using a mixture model of common ancestors. The method is an extension of substitution matrix-based probability estimation methods. In contrast to previous such methods, our method has a simple Bayesian interpretation and has the advantage over Dirichlet mixtures that it is both effective and simple to compute for large alphabets. The method is applied to estimate amino acid probabilities based on observed counts in an alignment and is shown to perform comparably to previous methods. The method is also applied to estimate probability distributions over protein families and improves protein classification accuracy.

Amino Acid Sequence↗

Conditional genotypic probabilities for microsatellite loci.

Modern forensic DNA profiles are constructed using microsatellites, short tandem repeats of 2-5 bases. In the absence of genetic data on a crime-specific subpopulation, one tool for evaluating profile evidence is the match probability. The match probability is the conditional probability that a random person would have the profile of interest given that the suspect has it and that these people are different members of the same subpopulation. One issue in evaluating the match probability is population differentiation, which can induce coancestry among subpopulation members. Forensic assessments that ignore coancestry typically overstate the strength of evidence against the suspect. Theory has been developed to account for coancestry; assumptions include a steady-state population and a mutation model in which the allelic state after a mutation event is independent of the prior state. Under these assumptions, the joint allelic probabilities within a subpopulation may be approximated by the moments of a Dirichlet distribution. We investigate the adequacy of this approximation for profiled loci that mutate according to a generalized stepwise model. Simulations suggest that the Dirichlet theory can still overstate the evidence against a suspect with a common microsatellite genotype. However, Dirichlet-based estimators were less biased than the product-rule estimator, which ignores coancestry.

Alleles↗

Reconstructing the prior probabilities of allelic phylogenies.

In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually "rare" topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4N(mu) (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions.

Algorithms↗

Rapid tracheal intubation with large-dose rocuronium: a probability-based approach.

UNLABELLED: There are situations in anesthesia in which it may be desirable to achieve rapid tracheal intubation with perfect conditions, i.e., no coughing or straining. To determine the dose of rocuronium that gives a high probability of achieving perfect conditions for rapid (within 60 s) tracheal intubation, we administered a range of doses of rocuronium, some larger than used previously. Sixty adults, anesthetized with thiopental 4 mg/kg IV and alfentanil 10 microg/kg IV, received rocuronium 0.4 to 2.0 mg/kg IV. We used logistic regression to define the relationship of rocuronium dose to probability of achieving perfect intubation conditions. We estimated the doses giving 90% and 95% probability of achieving perfect intubation and used resampling to determine confidence limits for these estimates. Rocuronium 1.85 and 2.33 mg/kg gave, respectively, 90% and 95% probability of perfect intubation conditions. The confidence limits (5th and 95th percentile) for these estimates were 1.15 to 2.31 and 1.23 to 3.22 mg/kg, respectively. In conclusion, it is possible to achieve perfect intubation conditions with large doses of rocuronium, but the long duration of action and expense may limit the usefulness of the technique. IMPLICATIONS: We found that it is possible to have a 90% probability of achieving perfect conditions for rapid tracheal intubation with large (up to 2.0 mg/kg) doses of rocuronium. These large doses of rocuronium may be useful in, for instance, head trauma or open globe injuries if succinylcholine is contraindicated.

Adult↗

Probability for human intake of an atom randomly released into ground, rivers, oceans and air.

Numerical estimates are developed for the probability of an atom randomly released in the top ground layers, in a river, or in the oceans to be ingested orally by a human, and for an atom emitted from an industrial source to be inhaled by a human. Estimates are obtained for both probability per year and for eventual probability. Results vary considerably for different elements, but typical values for total probabilities are: ground, 3 X 10(-3); oceans, 3 X 10(-4); rivers, 1.7 X 10(-4); and air, 5 X 10(-6). Probabilities per year are typically 1 X 10(-7) for releases into the ground and 5 X 10(-8) for releases into the oceans. These results indicate that for material with very long-lasting toxicity, it is important to include the pathways from the ground and from the oceans.

Aerosols↗

The probability that a specific cancer and a specified radiation exposure are causally related.

It is fundamental that a given cancer case cannot be attributed with absolute certainty to a prior ionizing radiation exposure, whatever the level of exposure. It is possible to estimate the probability of a causal relationship based on data and models that have been inferred from group statistics. Two types of information are needed to make these probability calculations: natural cancer incidence rates and risks of cancer induction from ionizing radiation. Cancer incidence rates for the United States are available in the report of the Surveillance, Epidemiology and End Results (SEER) program of the National Cancer Institute. Estimates of the risk of cancer induction from ionizing radiation have been published by the Advisory Committee on the Biological Effects of Ionizing Radiation (BEIR) of the National Academy of Sciences, the United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR), and the International Commission on Radiological Protection (ICRP). Using the parameters discussed above, the probability of causation formulation estimates the probability that a person who develops a particular cancer after a known quantifiable radiation exposure has the cancer as a result of the exposure. In 1985, the National Institutes of Health, responding to a U.S. Congressional mandate, published radioepidemiologic tables using the probability-of-causation method.

Humans↗

A review of probability of causation and its use in a compensation scheme for nuclear industry workers in the United Kingdom.

The assumption that any additional exposure to ionizing radiation leads to an increase in the risk of stochastic health effects implies that some cases of these effects will be caused by exposure incurred occupationally. The main health effect expected to arise in the exposed individuals is cancer. Such radiation-induced cancers cannot be distinguished from the far larger number of background cancers, and, therefore, causation must be assessed statistically. The probability of causation methodology has been developed to ascertain the likelihood that a particular cancer may be attributed to a particular prior exposure to radiation. Given the pertinent details of an individual case, a probability of causation value is calculated from the appropriate relative risk obtained from radiation risk models derived from the epidemiological study of exposed populations, although there are many uncertainties inherent in a particular probability of causation calculation. In the United Kingdom, the Compensation Scheme for Radiation-linked Diseases has been created to determine whether those individuals occupationally exposed to radiation in the nuclear industry who have subsequently developed a malignant disease should be compensated. The Scheme is a voluntary arrangement based upon the probability of causation methodology, which incorporates various procedures agreed by employer and employee representatives and their advisers. In a pragmatic approach to compensation, the uncertainties of a specific probability of causation calculation are accommodated through generosity factors which favor the claimant and encourage the use of the Scheme. The Scheme, which was introduced in 1982 and modified in 1987 and 1991 in the light of operational experience and revised risk estimates, has provided a successful alternative to litigation from the point of view of both employer and employee.

Humans↗

Probability of early repeat Pap smear in an integrated cervical screening programme.

The integration of routine Pap smear practice based on self-referral into an organized programme based on personal invitation is the recommended approach to cervical cancer screening. In this study, the cytology archive of the integrated cervical screening programme implemented in the Faenza district (northern Italy) was used to compare the population of women responding to invitation with that of self-referred women for the cumulative probability of early (< 36 months) repeat Pap smear after a negative result. Between 1995 and 1998, women aged 25-64 living in five municipalities of the district were targeted by the first round of the programme. Eligible for the study were 2356 women responding to invitation for screening and 2221 women not invited because of self-referral for Pap smear at any other setting. The probability of early repeat Pap smear was estimated by the life table method. Differences were evaluated by the Gehan test. Multivariate determinants were assessed by the Cox regression analysis. At 36 months' follow-up, the cumulative probability of early repeat Pap smear was 44% among self-referred women and 6% among women responding to invitation (relative hazard = 4.8). For self-referred women, the probability was related to age (with a peak at 35-44 years), previous Pap smear history and municipality of residence. Among women responding to invitation, only an inverse association with age was demonstrated. In conclusion, the observed differences in overall probability and determinants of early repeat Pap smear between the two screening populations provided important information on Pap smear usage in the total target population.

Adult↗