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PubMed2024

Leveraging clinical intuition to improve accuracy of phenotype-driven prioritization.

PURPOSE: Clinical intuition is commonly incorporated into the differential diagnosis as an assessment of the likelihood of candidate diagnoses based either on the patient population being seen in a specific clinic or on the signs and symptoms of the initial presentation. Algorithms to support diagnostic sequencing in individuals with a suspected rare genetic disease do not yet incorporate intuition and instead assume that each Mendelian disease has an equal pretest probability. METHODS: The LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL) algorithm calculates the likelihood ratio of clinical manifestations represented by Human Phenotype Ontology terms to rank candidate diagnoses. The initial version of LIRICAL assumed an equal pretest probability for each disease in its calculation of the posttest probability (where the test is diagnostic exome or genome sequencing). We introduce Clinical Intuition for Likelihood Ratios (ClintLR), an extension of the LIRICAL algorithm that boosts the pretest probability of groups of related diseases deemed to be more likely. RESULTS: The average rank of the correct diagnosis in simulations using ClintLR showed a statistically significant improvement over a range of adjustment factors. CONCLUSION: ClintLR successfully encodes clinical intuition to improve ranking of rare diseases in diagnostic sequencing. ClintLR is freely available at https://github.com/TheJacksonLaboratory/ClintLR.

Humans↗
PubMed1995

Using the standard staircase to measure the point of subjective equality: a guide based on computer simulations.

In experiments that measure a point of subjective equality, it is necessary to employ a psychophysical technique that measures the 50% point (P50) on the psychometric function. The standard staircase is an attractive candidate, because its simplicity makes it easy to understand and implement. However, Pentland (1980, Perception & Psychophysics, 28, 377-379) found his own maximum likelihood method (Best PEST) to be considerably less variable than the standard staircase. Here, computer simulations were used to study the effects of manipulating several parameters of the standard staircase in order to try to find a variant that would be competitive with the performance of Best PEST. A graphical summary of some of the standard staircase implementations that were found to be most stable is presented in order that investigators may choose easily the parameters best suited to their requirements. A comparison with an implementation of Pentland's Best PEST failed to replicate Pentland's finding, suggesting that investigators should have no misgivings about the standard staircase in experiments that measure a point of subjective equality.

Algorithms↗
PubMed1992

Longitudinal studies with continuous responses.

The analysis of serial measurements obtained in longitudinal studies plays an increasingly prominent role in applied research. The last few years have seen the development of many new techniques for carrying out analyses, including computer software. These methods can be used in a variety of standard problems, including repeated measures and cross-over designs, as well as growth curve analyses. We review these new methods, their application, and available computer packages. Data from a longitudinal study of lung function is used to illustrate the methods.

Adolescent↗
PubMed2026

Statistical test to compare the linkage model and the admixture model based on central limit results.

In the Admixture Model, the probability that an individual carries a certain allele at a specific marker depends on the allele frequencies in K ancestral populations and the proportion of the individual's genome originating from these populations. The markers are assumed to be independent. The Linkage Model is a Hidden Markov Model that extends the Admixture Model by incorporating linkage between neighboring loci. We prove consistency and asymptotic normality of maximum likelihood estimators for the ancestry of individuals in the Linkage Model, complementing earlier results by (Pfaff et al., 2004; Pfaffelhuber and Rohde, 2022; Heinzel, 2025) for the Admixture Model. These results are used to prove that a statistical test that allows for model selection between the Admixture Model and the Linkage Model is an asymptotic level-α-test. Finally, we demonstrate the practical relevance of our results by applying the test to real-world data from The 1000 Genomes Project Consortium (2015).

Genetic Linkage↗
PubMed1986

Plicatic acid-specific IgE and nonspecific bronchial hyperresponsiveness in western red-cedar workers.

In a cross-sectional survey of 652 workers in a western red-cedar sawmill, we obtained data on symptoms, pulmonary function, immediate skin reactivity to common allergens, nonspecific bronchial responsiveness, total IgE level, and sensitization to plicatic acid conjugated with human serum albumin as measured by RAST. Dust exposure was estimated by personal and area sampling for total dust during a work shift and cumulative exposure by duration of employment. Seven percent of the workers had an elevated RAST, and 20% had nonspecific bronchial hyperresponsiveness. Elevation in RAST was associated with bronchial hyperresponsiveness. Almost half (46%) of the workers with RAST elevation had bronchial hyperresponsiveness compared to 18% in workers with no RAST elevation. The association was unaffected by total IgE level or by limiting the analysis to workers without respiratory symptoms and was most apparent in younger workers. Bronchial hyperresponsiveness was associated with increased prevalence of respiratory symptoms as well as with lower levels of pulmonary function. The likelihood of bronchial hyperresponsiveness increased with increasing age but was unrelated to the dust-exposure concentration. RAST elevation was unrelated to employment duration or dust exposure and was not associated with an increased prevalence of symptoms or lower levels of pulmonary function independent of bronchial hyperresponsiveness. We conclude that plicatic acid-specific IgE and nonspecific bronchial hyperresponsiveness are associated in western red-cedar workers and that this association may reflect a causal connection.

Adult↗
PubMed1976

Prognosis for recovery of function in acute renal failure. Value of the renal image obtained using iodohippurate sodium I 131.

Twenty-four survivors of acute, nonobstructive, nonnephritic renal failure had a renal scan using iodohippurate sodium I 131 performed early in the acute illness. Scans were judged according to whether the renal images were prominent, faint, or absent during the first 30 minutes after intravenous injection of 100 to 250 microcuries of iodohippurate sodium I 131. All ten patients with prominent renal images attained life-sustaining renal function with an average postrecovery creatinine clearance of 80 ml/min. Of the seven patients with faint renal images, six recovered life-sustaining renal function (average creatinine clearance of 39 ml/min), and one required chronic hemodialysis. Seven patients had no renal image initially; four recovered life-sustaining renal function with an average creatinine clearance of 25 ml/min; three required chronic hemodialysis. We conclude that, for patients with acute renal failure, the appearance of the renal image obtained using this substance is an important indicator of renal viability and of the likelihood for functional recovery.

Acute Kidney Injury↗
PubMed1992

On identifying a positive dose-response surface for combination agents.

This article concerns construction of a confidence surface for tangential slopes of the dose-response surface of a combination therapy to identify where response increases as a function of drug dosage. This approach extends to the assessment of the effectiveness of the combination therapy.

Dose-Response Relationship, Drug↗
PubMed1994

Dust exposure indices and lung function changes in longshoremen and dock workers.

A group of Dutch harbor workers involved in loading and unloading bulk products from sea vessels such as coal, cokes, and some other products like alumina, borax, phosphate ore, and vermiculite was studied. Exposures were characterized by personal and environmental monitoring. This information was subsequently used to estimate several dust exposure indices and to study relationships with lung function variables and respiratory symptoms. Average respirable dust exposure levels ranged from 0.3-4.0 mg/m3. Workers involved in unloading products from sea vessels were exposed to the highest dust levels. Supervisors and workers with tasks in the dock had an intermediate to low exposure. Office workers had the lowest exposure to respirable dust. Inhalable dust levels were considerably higher and average exposures ranged from 0.3-80 mg/m3. The ranking of occupational titles by inhalable dust exposure was almost identical to the rank order of respirable dust levels. Workers with higher current and cumulative dust exposures tended to have a lower lung function, and only shortness of breath had a statistically significant relationship with current and cumulative inhalable dust exposure. In general, relationships between lung function and inhalable dust levels tended to be somewhat stronger in terms of statistical significance, because inhalable dust is an estimate of dust deposition in the upper airways and lung function is a measurable parameter of airway obstruction in that region. However, the differences with respirable dust were minimal, and variability in dust exposure levels was extremely large for this population. It was concluded that harbor workers involved in unloading ships containing coal and various kinds of ore can be exposed to high dust levels. Relationships between dust exposure and lung function illustrate that these exposures are a respiratory hazard. Our finding that inhalable dust levels have a somewhat stronger relationship with lung function level than respirable dust levels deserves further attention.

Adult↗
PubMed1992

A random dipole model for spontaneous brain activity.

The statistical properties of the EEG and the MEG are described mathematically as the result of randomly distributed dipoles. These dipoles represent the interactions of cortical neurons. For certain dipole distributions, the first- and second-order moments of the electric and magnetic fields are derived analytically. If the dipoles are in a spherical volume conductor and have no preference for any direction, the variance of a differentially measured EEG-signal is only a function of the electrode distance. In this paper, the theoretically derived variance function will be compared with EEG- and MEG-measurements. It is shown that a dipole with a fixed position and a randomly fluctuating amplitude is an adequate model for the alpha-rhythm. An expression for the covariance between the magnetic field and a differentially measured EEG-signal is derived. This covariance is considered as a function of the magnetometer position, and is compared with the measurements of Chapman et al. [23]. The theory can be used to obtain a (spatial) covariance matrix of the background noise, which occurs in evoked potential measurements. Such a covariance matrix can be used to obtain a maximum likelihood estimator of the dipole parameters in evoked potential studies, to evaluate the merits of the so-called "Laplacian derivation," and for the interpolation of electromagnetic data.

Artifacts↗
PubMed1989

Determination of characteristic parameters of human postural dynamics.

Posture control performance was quantified in three variables (swiftness, stiffness, damping). Subjects were tested with a force platform recording body sway induced by vibrators attached to the calf muscles. Parameter estimation was made with identification of a transfer function representing the stabilized inverted pendulum. It is conjectured that the state feedback parameters identified are suitable for use in assessing ability to maintain posture.

Adult↗
PubMed1995

Cognitive function and assessment of lung function in the elderly.

The feasibility of spirometry or respiratory impedance measurements for assessing lung function in the elderly was compared in 208 institutionalized patients with various degrees of cognitive function impairment. Respiratory impedance was determined by the forced oscillation technique. Cognitive function was assessed by the score for the mini-mental state (MMS) examination. Of the 208 patients, 126 had severe cognitive impairment (MMS < or = 17), 36 had mild impairment (18 < or = MMS < or = 23), and 46 had no impairment (MMS > or = 24). Of the 208 patients, respiratory impedance measurements were possible in 159, whereas in only 85 was spirometry possible. The overall difference between the feasibility rates for the spirometric and respiratory impedance measurements was highly significant (chi 2 = 71.4; p < 10(-6)). The difference between the feasibility rates for the two techniques was higher in the group of subjects with severe cognitive impairment than in the groups with mild impairment and no impairment, respectively. Among the 84 patients able to complete both tests, significant correlations were found between the spirometric and respiratory impedance measurements. These results indicate that respiratory impedance measurement seems a more useful tool than spirometry for assessing lung function in elderly patients whenever cognitive function is impaired.

Aged↗
PubMed2025

Penalized likelihood optimization for censored missing value imputation in proteomics.

Label-free bottom-up proteomics using mass spectrometry and liquid chromatography has long been established as one of the most popular high-throughput analysis workflows for proteome characterization. However, it produces data hindered by complex and heterogeneous missing values, which imputation has long remained problematic. To cope with this, we introduce Pirat, an algorithm that harnesses this challenge using an original likelihood maximization strategy. Notably, it models the instrument limit by learning a global censoring mechanism from the data available. Moreover, it estimates the covariance matrix between enzymatic cleavage products (ie peptides or precursor ions), while offering a natural way to integrate complementary transcriptomic information when multi-omic assays are available. Our benchmarking on several datasets covering a variety of experimental designs (number of samples, acquisition mode, missingness patterns, etc.) and using a variety of metrics (differential analysis ground truth or imputation errors) shows that Pirat outperforms all pre-existing imputation methods. Beyond the interest of Pirat as an imputation tool, these results pinpoint the need for a paradigm change in proteomics imputation, as most pre-existing strategies could be boosted by incorporating similar models to account for the instrument censorship or for the correlation structures, either grounded to the analytical pipeline or arising from a multi-omic approach.

Proteomics↗
PubMed1992

Multidimensional ordering of psychopathology. A factor-analytic study using the Comprehensive Psychopathological Rating Scale.

The aim of the study was to search for a multidimensional order in the psychopathology of the functional mental disorders in general. A heterogeneous group of 192 patients was investigated by means of a semistructured interview based on the Comprehensive Psychopathological Rating Scale. Principal component factor analysis revealed 5 clinically meaningful dimensions interpretable as representing dysregulation of emotion and motivation, perceptual and behavioural disintegration and dysregulation of autonomic functions.

Adolescent↗
PubMed1994

Handling covariates in population pharmacokinetics.

Population models were developed to analyze processes, described by parametric models, from measurements obtained in a sample of individuals. In order to analyze the sources of interindividual variability, covariates may be incorporated in the population analysis. The exploratory analyses and the two-stage approaches which use standard non-linear regression techniques are simple tools to select meaningful covariates. The global population approaches may be divided into two classes within which the covariates are handled differently: the parametric and the non-parametric methods. The power as well as the limitations of each approach regarding handling of covariates are illustrated and compared using the same data set which concerns the pharmacokinetics of gentamicin in neonates. With parametric approaches a second-stage model between structural parameters and covariates has to be defined. In the non-parametric method the joint distribution of parameters and covariates is estimated without parametric assumptions; however, it is assumed that covariates are observed with some error and parameters involved in functional relationships are not estimated. The important results concerning gentamicin in neonates were found by the two methods.

Age Factors↗
PubMed1979

The discriminative efficiency of the Bayley Scales of Infant Development.

This study was designed to determine the discriminative efficiency of the Bayley Mental and Motor Scales for classifying infants as neurologically suspicious and neurologically normal. The two groups employed in the study were formed on the basis of the results from comprehensive neurological examinations performed at ages 1 and 7. Three discriminant function analyses were conducted, one for each scale separately and a third incorporating both scales using a stepwise procedure. Efficiency was measured in terms of number of correct and incorrect classifications, false positive and false negative errors, and validity coefficients. Comparisons among the analyses were examined by means of relative discrimination power and incremental validity. The findings suggested that the Motor Scale provides the most accurate identification of infants with suspected neurological impairments. A statistically significant likelihood discriminant function derived from both scales yielded some additional discriminative power. The law of parsimony, however, dictated the use of the single Motor Scale.

Child↗
PubMed1994

Utility of the force of infection model for assessing changes in the dynamics of bancroftian filarial infections.

Force of infection is measured in terms of the number of effective contacts that have been introduced into the population by infective vectors. The utility of such a measure in describing the dynamics of bancroftian filarial infection was tested. Force of infection (beta) incorporating the durations of patent period and pre-patent period was estimated for different age classes (assuming that it is constant in that particular age class) and it was found that the predicted post-control prevalences were close to the observed figures. Utility of Remme's model in areas with different transmission levels is discussed. It was examined whether the empirical function generally used in helminth infections to describe the functional relationship between beta and age could be used for lymphatic filariasis. The relationship between the two was not adequately described by the function. Force of infection, when compared with rate of acquisition calculated using longitudinal data, showed that this measure could be used as a crude estimate of rate of acquisition in places which do not have longitudinal data sets.

Adolescent↗
PubMed1994

Transmitting males and carrier females in fragile X--revisited.

Fragile X "transmitting males" have customarily been defined as phenotypically normal hemizygotes, who show very few or no fragile sites, and who transmit the fragile X premutation to phenotypically normal daughters. However, an objective justification of this definition was lacking. The discovery of an unstable CCG repeat as the genetic basis of fragile X further emphasized the apparent distinction between the "normal transmitting males" with short repeat and expression of the FMR1 gene, and the affected males with larger repeats (delta > 0.6 kb) and a complete lack of FMR1 transcription. We have recently shown that the transition between these two groups in phenotypic expression of fragile X is gradual, mainly on account of methylation mosaicism. However, there were insufficient data on the phenotype within the short repeat (0.0 < delta < 0.6) range. In this paper we approach this problem by comparing some clinical, anthropometric, and psychometric data from a sample of normal transmitting males with those from their non-fragile X male relatives. Moreover, female carriers with short repeat are compared for the same traits with their non-fragile X female relatives. The results have shown that both males and females with a short repeat differed significantly from normal on several psychometric and physical measurements, and males only showed differences in typical facial traits. Further studies of genotype-phenotype correlations within the short repeat range, including the estimate of FMR1 gene function and a more exact estimate of repeat size, is required before genetic explanation for the clinical findings can be provided.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗