TreeQTL: hierarchical error control for eQTL findings.

UNLABELLED: : Commonly used multiplicity adjustments fail to control the error rate for reported findings in many expression quantitative trait loci (eQTL) studies. TreeQTL implements a hierarchical multiple testing procedure which allows control of appropriate error rates defined relative to a grouping of the eQTL hypotheses. AVAILABILITY AND IMPLEMENTATION: The R package TreeQTL is available for download at http://bioinformatics.org/treeqtl CONTACT: sabatti@stanford.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Selective correlations; not voodoo.

The problem of "voodoo" correlations-exceptionally high observed correlations in selected regions of the brain-is well recognized in neuroimaging. It arises when quantities of interest are estimated from the same data that was used to select them as interesting. In statistical terminology, the problem of inference following selection from the same data is that of selective inference. Motivated by the unwelcome side-effects of splitting the data- the recommended remedy-we adapt the recent developments in selective inference in order to construct confidence intervals (CIs) with good reproducibility prospects, even if selection and estimation are done with the same data. These intervals control the expected proportion of non-covered correlations in the selected voxels-the False Coverage Rate (FCR). They extend further toward zero than standard intervals, thus attenuating the impression made by highly biased observed correlations. They do so adaptively, in that they coincide with the standard CIs when far away from the selection point. We complement existing analytic proofs with a simulation, showing that the proposed intervals control the FCR in realistic social neuroscience problems. We also suggest a "confidence calibration plot", to allow the intervals to be reported in a clear and interpretable way. Applying the proposed methodology on a loss-aversion study, we demonstrate that with the sample size and selection type employed, selection bias is considerable. Finally, selective intervals are compared to the currently recommended data-splitting approach. We discover that our approach has more power and typically more informative, as no data is discarded. Computation of the intervals is implemented in an accompanying software package.

Pharmacokinetics of buprenorphine following intravenous and buccal administration in cats, and effects on thermal threshold.

This study reports the pharmacokinetics of buprenorphine, following i.v. and buccal administration, and the relationship between buprenorphine concentration and its effect on thermal threshold. Buprenorphine (20 µg/kg) was administered intravenously or buccally to six cats. Thermal threshold was determined, and arterial blood sampled prior to, and at various times up to 24 h following drug administration. Plasma buprenorphine concentration was determined using liquid chromatography/mass spectrometry. Compartment models were fitted to the time-concentration data. Pharmacokinetic/pharmacodynamic models were fitted to the concentration-thermal threshold data. Thermal threshold was significantly higher than baseline 44 min after buccal administration, and 7, 24, and 104 min after i.v. administration. A two- and three-compartment model best fitted the data following buccal and i.v. administration, respectively. Following i.v. administration, mean ± SD volume of distribution at steady-state (L/kg), clearance (mL·min/kg), and terminal half-life (h) were 11.6 ± 8.5, 23.8 ± 3.5, and 9.8 ± 3.5. Following buccal administration, absorption half-life was 23.7 ± 9.1 min, and terminal half-life was 8.9 ± 4.9 h. An effect-compartment model with a simple effect maximum model best predicted the time-course of the effect of buprenorphine on thermal threshold. Median (range) ke0 and EC50 were 0.003 (0.002-0.018)/min and 0.599 (0.073-1.628) ng/mL (i.v.), and 0.017 (0.002-0.023)/min and 0.429 (0.144-0.556) ng/mL (buccal).

Bioavailability of morphine, methadone, hydromorphone, and oxymorphone following buccal administration in cats.

Buccal administration of buprenorphine is commonly used to treat pain in cats. It has been argued that absorption of buprenorphine through the buccal mucosa is high, in part due to its pKa of 8.24. Morphine, methadone, hydromorphone, and oxymorphone have a pKa between 8 and 9. This study characterized the bioavailability of these drugs following buccal administration to cats. Six healthy adult female spayed cats were used. Buccal pH was measured prior to drug administration. Morphine sulfate, 0.2 mg/kg IV or 0.5 mg/kg buccal; methadone hydrochloride, 0.3 mg/kg IV or 0.75 mg/kg buccal; hydromorphone hydrochloride, 0.1 mg/kg IV or 0.25 mg/kg buccal; or oxymorphone hydrochloride, 0.1 mg/kg IV or 0.25 mg/kg buccal were administered. All cats received all treatments. Arterial blood was sampled immediately prior to drug administration and at various times up to 8 h thereafter. Bioavailability was calculated as the ratio of the area under the time-concentration curve following buccal administration to that following IV administration, each indexed to the administered dose. Mean ± SE (range) bioavailability was 36.6 ± 5.2 (12.7-49.5), 44.2 ± 7.9 (18.7-70.5), 22.4 ± 6.9 (6.4-43.4), and 18.8 ± 2.0 (12.9-23.5)% for buccal administration of morphine, methadone, hydromorphone, and oxymorphone, respectively. Bioavailability of methadone was significantly higher than that of oxymorphone.

Revisiting multi-subject random effects in fMRI: advocating prevalence estimation.

Random effect analysis has been introduced into fMRI research in order to generalize findings from the study group to the whole population. Generalizing findings is obviously harder than detecting activation within the study group since in order to be significant, an activation has to be larger than the inter-subject variability. Indeed, detected regions are smaller when using random effect analysis versus fixed effects. The statistical assumptions behind the classic random effect model are that the effect in each location is normally distributed over subjects, and "activation" refers to a non-null mean effect. We argue that this model is unrealistic compared to the true population variability, where due to function-anatomy inconsistencies and registration anomalies, some of the subjects are active and some are not at each brain location. We propose a Gaussian-mixture-random-effect that amortizes between-subject spatial disagreement and quantifies it using the prevalence of activation at each location. We present a formal definition and an estimation procedure of this prevalence. The end result of the proposed analysis is a map of the prevalence at locations with significant activation, highlighting activation regions that are common over many brains. Prevalence estimation has several desirable properties: (a) It is more informative than the typical active/inactive paradigm. (b) In contrast to the usual display of p-values in activated regions - which trivially converge to 0 for large sample sizes - prevalence estimates converge to the true prevalence.

Non-linear formulas for the spinal cord injury ability realization measurement index.

STUDY DESIGN: The spinal cord injury ability realization measurement index (SCI-ARMI) assesses rehabilitation potential and efficacy based on the linear relationship between the Spinal Cord Independence Measure (SCIM) and the American Spinal Injury Association impairment scale (AIS) motor scores (AMS). OBJECTIVES: The objective of this study is to develop new SCI-ARMI formulas using a more flexible approach that is less sensitive to the distribution of the AMS score among spinal cord lesion (SCL) patients. SETTING: Loewenstein Rehabilitation Hospital, Raanana, and the Statistical Laboratory, School of Mathematics, Faculty of Exact Sciences, Tel-Aviv University, Israel. METHODS: SCIM III and AMS of 226 Israeli SCL patients were monitored. Linear formulas, quadratic formulas and non-parametric formulas were estimated to express the relationship between the 95th percentile of the SCIM III values for patients with given AMS at discharge from rehabilitation (SCIM95) and the corresponding AMS value. This relationship was used to calculate SCI-ARMI values, defined as the ratio of the observed SCIM score and the respective SCIM95 for a given patient's AMS score. RESULTS: The estimated quadratic formula for the relationship between the 95th percentile of the SCIM III and the AMS score was found to be most appropriate, and formulas are provided for SCIM95 calculation in the various areas of function. The use of these formulas to calculate SCI-ARMI values is presented. CONCLUSION: The new formulas improve the accuracy of calculated ability realization for any AMS. The new statistical procedure will be used for the upcoming data analysis of a larger-scale international SCI-ARMI study.

A new grading for easy and concise description of functional status after spinal cord lesions.

BACKGROUND: Disability scales do not enable the transmission of concise, meaningful and daily function description for clinical purposes. STUDY DESIGN: Cross-sectional statistical analysis of 328 patients' Spinal Cord Independence Measure (SCIM) III item scores (SIS). OBJECTIVE: To develop a concise and clinically interpretable data-based characterization of daily task accomplishment for patients with spinal cord lesions (SCLs). SETTING: Multi-center study at 13 spinal units in 6 countries. METHODS: Patients were grouped into clusters characterized by smaller differences between the patients' SIS within the clusters than between their centers, using the k-medoides algorithm. The number of clusters (k) was chosen according to the percent of SIS variation they explained and the clinical distinction between them. RESULTS: Analysis showed that k=8 SIS clusters offer a good description of the patient population. The eight functional clusters were designated as A-H, each cluster (grade) representing a combination of task accomplishments. Higher grades were usually (but not always) associated with patients implementing more difficult tasks. Throughout rehabilitation, the patients' functional grade improved and the distribution of patients with similar functional grades within the total SCIM III score deciles remained stable. CONCLUSIONS: A new classification based on SIS clusters enables a concise description of overall functioning and task accomplishment distribution in patients with SCL. A software tool is used to identify the patients' functional grade. Findings support the stability and utility of the grades for characterizing the patients' functional status.

Estimating wall guidance and attraction in mouse free locomotor behavior.

In this study, we estimate the influence exerted by the wall of the Open Field on the trajectory of the mouse. The wall exerts two types of influence on the mouse's path: one of guidance and one of attraction. The guiding influence is expressed by the tendency of mice to progress in parallel to the wall. This tendency wanes with increasing distance from the wall but is observed at large distances from it. The more parallel the mouse is to the wall the higher is its speed, even when distant from the wall. This association between heading direction and speed shows that the mouse controls its heading in reference to the wall. It is also observed in some blind strains, revealing that wall-guidance is not based exclusively on vision. The attraction influence is reflected by movement along the wall and by the asymmetry between speed during movement toward, and during movement away from the wall: sighted mice move faster toward the wall, whereas blind mice use similar speeds in both directions. Measures characterizing these influences are presented for five inbred strains, revealing heritable components that are replicable across laboratories. The revealed structure can lead to the identification of distinct groups of genes that mediate the distinct influences of guidance and attraction exerted by the wall. It can also serve as a framework for the decoding of electrophysiological data recorded in free moving rodents in the Open Field.

Wild mouse open field behavior is embedded within the multidimensional data space spanned by laboratory inbred strains.

The vast majority of studies on mouse behavior are performed on laboratory mouse strains (Mus laboratorius), while studies of wild-mouse behavior are relatively rare. An interesting question is the relationship between the phenotypes of M. laboratorius and the phenotypes of their wild ancestors. It is commonly believed, often in the absence of hard evidence, that the behavior of wild mice exceeds by far, in terms of repertoire richness, magnitude of variables and variability of behavioral measures, the behavior of the classical inbred strains. Having phenotyped the open field behavior (OF) of eight of the commonly used laboratory inbred strains, two wild-derived strains and a group of first-generation-in-captivity local wild mice (Mus musculus domesticus), we show that contrary to common belief, wild-mouse OF behavior is moderate, both in terms of end-point values and in terms of their variability, being embedded within the multidimensional data space spanned by laboratory inbred strains. The implication could be that whereas natural selection favors moderate locomotor behavior in wild mice, the inbreeding process tends to generate in mice, in some of the features, extreme and more variable behavior.

Rats and mice share common ethologically relevant parameters of exploratory behavior.

Detailed studies of rat exploratory behavior reveal that it consists of typical behavior patterns having a distinct structure. Recently we have developed interactive software that uses as input the automatically digitized time-series of the animal's location for the visualization, analysis, capturing and quantification of these patterns. We use this software here for the study of BALB/cJtau mouse behavior. The results suggest that a considerable number of rat patterns are also present in the mouse. These ethologically-relevant patterns have a significant potential as a phenotyping tool.

Controlling the false discovery rate in behavior genetics research.

The screening of many endpoints when comparing groups from different strains, searching for some statistically significant difference, raises the multiple comparisons problem in its most severe form. Using the 0.05 level to decide which of the many endpoints' differences are statistically significant, the probability of finding a difference to be significant even though it is not real increases far beyond 0.05. The traditional approach to this problem has been to control the probability of making even one such error--the Bonferroni procedure being the most familiar procedure achieving such control. However, the incurred loss of power stemming from such control led many practitioners to neglect multiplicity control altogether. The False Discovery Rate (FDR), suggested by Benjamini and Hochberg [J Royal Stat Soc Ser B 57 (1995) 289], is a new, different, and compromising point of view regarding the error in multiple comparisons. The FDR is the expected proportion of false discoveries among the discoveries, and controlling the FDR goes a long way towards controlling the increased error from multiplicity while losing less in the ability to discover real differences. In this paper we demonstrate the problem in two studies: the study of exploratory behavior [Behav Brain Res (2001)], and the study of the interaction of strain differences with laboratory environment [Science 284 (1999) 1670]. We explain the FDR criterion, and present two simple procedures that control the FDR. We demonstrate their increased power when used in the above two studies.

Cyproheptadine versus propranolol for the treatment of acute neuroleptic-induced akathisia: a comparative double-blind study.

The purpose of this study was to investigate the efficacy of cyproheptadine, an antiserotonergic agent, in the treatment of neuroleptic-induced akathisia (NIA), as compared with propranolol, the current gold standard. In a double-blind trial, 30 patients with schizophrenia and NIA received either cyproheptadine 16 mg/day (N = 18) or propranolol 80 mg/day (N = 12) for 4 days, followed by 3 days without any anti-NIA treatment. The Barnes Akahisia Scale, Simpson-Angus Extrapyramidal Effects Rating Scale, and Brief Psychiatric Rating Scale were used to assess the severity of NIA, parkinsonism, and psychosis, respectively. In both groups, the severity of NIA decreased significantly over time (cyproheptadine, -46%; propranolol, -42%), with no significant intergroup difference. The NIA symptoms worsened significantly when cyproheptadine and propranolol were discontinued. We conclude that cyproheptadine 16 mg/day is as effective as propranolol for the treatment of acute NIA. The antiakathisic effect of cyproheptadine may be mostly attributable to its serotonin antagonistic activity.

Statistical discrimination of natural modes of motion in rat exploratory behavior.

We analyze the locomotor behavior of the rat during exploration, and show that digitally collected data (time series of positions) provide a sufficient basis for establishing that the rat uses several distinct modes of motion (first, second, third, and sometimes fourth gear). The distinction between these modes is obtained by first segmenting the time series into sequences of data points occurring between arrests (as ascertained within the resolution of the data acquisition system). The statistical distribution of the maximal amount of motion occurring within each of these episodes is then analyzed and shown to be multi modal. This enables us to decompose motion into distinct modes. In one application of this decomposition we show that the ethological ad hoc notion of stopping behavior corresponds to progression without leaving first gear. We do so by showing that the spatial spread of such progressions is confined to a small 20-50 cm range in a 6.5 m diameter arena. This provides a justification for a construct of 'staying in place'. This construct is not defined in terms of position in objective space, but purely in terms of the rat's own behavior. We test the generality of our method by applying it to mouse exploratory behavior.

The dynamics of long-term exploration in the rat. Part I. A phase-plane analysis of the relationship between location and velocity.

Rat exploratory behavior consists of regular excursions into the environment from a preferred place termed a home base. A phase plane representation of excursions reveals a geometrical pattern that changes during exploration in both shape and size. We first show that with time and repeated exposures to the same large environment there is a gradual increase in the length of excursions; each rat has its own characteristic length of excursions; but all rats share a similar rate of excursion growth. As in our experimental setup the rats perform increasingly longer paths from one location, while locomoting back and forth along the walls of the arena, exposure is more extensive at the proximal part of the route, and less at the distal part. We consequently show that the rat's velocity pattern changes concurrently with the increase in excursion length, and in correlation with the level of exposure (familiarity) to places. The primitive velocity pattern consists of slow progression while moving away from base and fast progression while returning to it. During exposure the asymmetry in velocity is inverted. The inversion spreads across successive excursions from the home base outwards. The rate of spread of this inversion is higher than the rate of increase in excursion length, and is similar across rats. Because it spreads more rapidly than the increase in excursion length, the global shape of the excursion trajectory changes. The dynamics of excursion shape share similar properties with the dynamics of excursion length. Both might reflect the same intrinsic constraints on the amount of novelty that a rat can handle per excursion.

The dynamics of long-term exploration in the rat. Part II. An analytical model of the kinematic structure of rat exploratory behavior.

A simple analytical model is proposed here that captures to a large extent the kinematic structure of rat exploratory behavior. Previous studies have shown that such behavior consists of regular excursions into the environment from a preferred place termed a home base. In the first part of this study, we showed that with time and repeated exposure to the same large environment, there is a gradual increase in the length of excursions. Concurrently, the rat's velocity pattern changes in a complex yet structured way, which is correlated with the exposure (= familiarity) to places. In this part, we show that the complex pattern described there might be explained by an analytic model, in terms of a simple dynamical system, with few assumptions concerning motivation and learning. The model is studied both by analysis and simulation. The theoretical examination of the dynamics of excursion length suggests that excursion length increases as a linear function of two system parameters, one governing the rate of motivation loss, and the other the rate of (location-specific) familiarization. Combining this theoretical finding with the empirical results suggests that the two theoretical parameters are linearly related: the less confident the rat, the slower its familiarization rate, and thus differences in patterns of movement between rats can be explained using one rat-specific parameter. Furthermore, the more complex velocity pattern of the rat can then be easily captured by the same model. The analyzed behavior of the rat suggests that the locale sensory information that the rat collects has a gradient towards the home base, with decreasing information input away from home base. This sensory pattern emerges from the simple set of rules and restrictions on the rat's exploratory behavior. Thus, instead of imposing a set of ad hoc restrictions on a simulated rat so that its spatial learning is similar to that of a real rat, the model suggests a set of simple intrinsic constraints to govern the exploratory behavior.

Coordination of side-to-side head movements and walking in amphetamine-treated rats: a stereotyped motor pattern as a stable equilibrium in a dynamical system.

Rats injected with 5.0 mg/kg (+)-amphetamine perform, at one stage of the drug's influence, rhythmic side-to-side head movements while walking. This makes them an interesting preparation for investigating how stereotyped motor patterns emerge from the coordination of periodic movements. We report here such a pattern we have isolated: the left foreleg and the right hindleg land on the ground as the head reaches the peak of its movement to the right, and vice versa (contra-lateral pattern). We show that this pattern can be explained as a stable equilibrium in a simple, nonlinear dynamical model, similar to models developed for tapping with both hands in human subjects. The model also accounts for sequences of behavior that are not in the contra-lateral pattern, explaining them as a flow of the system back towards the stable equilibrium after a disturbance. Motor patterns that constitute the building blocks of unconstrained behavior are often defined as fixed phase relations between movements of the parts of the body. This study applies the paradigm of Dynamic Pattern Generation to free (unconstrained) behavior: motor patterns are defined as stable equilibria in dynamical systems, assembled by mutual influence of concurrent movements. Our findings suggest that this definition is more powerful for the description of free behavior. The amphetamine-treated rat is a useful preparation for investigating this notion in an unconstrained animal whose behavior is still not as complex and variable as that of the normal animal.

Mathematical formulae for the prediction of the residual beta cell function during the first two years of disease in children and adolescents with insulin-dependent diabetes mellitus.

On the basis of a retrospective study of 71 children followed for 24 months after diagnosis of type I insulin dependent diabetes a fitted mathematical model was constructed for the prediction of the course of beta cell function from the time of diagnosis. Two equations were derived, one for the maximal basal (B-max) and the other for the maximal i.v. glucagon stimulated peak C-peptide (P-max) levels reached during the remission period. The prognostic variables selected for analysis were: peak C-peptide levels at diagnosis (Po), age sex, degree of obesity, pubertal rating, the presence of islet cell antibodies (ICA) and levels of GHb. Multivariate analysis of the data showed that Po (p = 0.0006), puberty (p = 0.041). obesity (p = 0.0021), sex (p = 0.031), ICA (p = 0.0045) and GHb(p = 0.0066) significantly contributed to the prediction formula obtained for B-max whereas the contribution of the above variables for P-max were: Po (p = 0.0019), puberty (p = 0.0187), obesity (p = 0.0058), sex (p = 0.0598), ICA (p = 0.0187) and GHb (p = 0.0027). The residuals of the observed values from the values fitted by the predicted equations served to define two separate groups demonstrating distinct differences in the natural course of beta cell function in type I diabetes. This fitted model may thus be useful in distinguishing between newly diagnosed young patients who will undergo remission, requiring lower insulin doses, and those who have little chance for remission. It might also be helpful in the selection of patients most likely to benefit from immunosuppression or modulation, to maximize the benefit to risk ratio for such patients.

Insulin antibody assay: a statistical evaluation of sensitivity, precision and reproducibility in healthy subjects.

Eighty-seven sera from healthy non-diabetic subjects, negative for islet cell antibodies, were analysed for 125I-insulin serum binding capacity by a commercial radioimmunoassay. In order to define the detection limit of the assay for insulin antibodies we used the corrected binding capacity to 125I-insulin of the normal sera obtained by competitive inhibition with excess of unlabelled insulin. To test the reproducibility of the results as a function of the tracer decay the sera were re-examined after intervals of 17 and 37 days, when a drift of more than 1% was found in the period investigated. Using the corrected bindings improved reproducibility considerably. The extra variation between the three assays, taking into account the decay of the tracer, was negligible. The main component of error contributing to these variations among individuals was found to be the precision, defined as the mean standard deviation among the replicates, which is SD(c) = 0.325%. We conclude that this assay is suitable for the screening of positive insulin autoantibodies in pre-diabetic subjects, and recommend that the estimate of precision from the replicates with excess insulin be used and that the detection limit be set at three times the estimated SD(c).

Stopping behavior: constraints on exploration in rats (Rattus norvegicus).

In the absence of an obvious reference place, rat locomotor behavior in a novel environment appears haphazard. In previous work, one or two places termed home bases, were shown to stand out from all the other places in the environment in terms of the behaviors performed in them and in terms of their behavioral stability. We use home base location as a reference place for rat movement in locale space, by defining an excursion as a trip starting at a home base and ending at the next stop at a home base. We then establish the uniform distribution as an appropriate model for the number of stops per excursion. This way we show that there is an intrinsic upper bound on the number of times a rat stops during an excursion. As a rat leaves the home base, home base attraction increases with every additional stop performed by it, first slowly and then fast. This cumulative process of attraction may be concluded after each stop, as long as the number of stops does not exceed an intrinsic upper bound; once the upper bound is reached, the rat concludes that excursion and returns to base. The session's upper bound does not increase with the size of the explored area.

Paradoxical pharmacodynamic effect of atropine on parasympathetic control: a study by spectral analysis of heart rate fluctuations.

The power spectrum of instantaneous heart rate fluctuations was used to determine the optimal doses of atropine that induce a maximal vagolytic or vagomimetic effect. In a crossover placebo controlled study, eight volunteers received increasing bolus doses of intravenous atropine (0.1 to 2.3 mg per subject) or placebo, and frequency bands of the power spectrum were integrated. During atropine administration a significant bimodal dose dependence was observed for the respiratory peak (0.2 to 0.4 Hz, p = 0.0006), the midfrequency band (0.09 to 0.15 Hz, p = 0.0035), and mean heart rate (p < 0.0001). Low doses (< 0.4 mg per subject) increased the respiratory and midfrequency band power, with maximal response at 0.2 mg per subject. Larger doses of atropine, 0.5 to 2.3 mg per subject, markedly reduced the power in all frequency bands in a dose-dependent way. The corresponding changes in mean heart rate were simultaneous, but in the opposite direction. We suggest that the respiratory peak of the power spectrum can be used to optimize drug effects on cardiac parasympathetic control.