Case‐control data analysis for randomly pooled biomarkers

Pooled study designs, where individual biospecimens are combined prior to measurement via a laboratory assay, can reduce lab costs while maintaining statistical efficiency. Analysis of the resulting pooled measurements, however, often requires specialized techniques. Existing methods can effectively estimate the relation between a binary outcome and a continuous pooled exposure when pools are matched on disease status. When pools are of mixed disease status, however, the existing methods may not be applicable. By exploiting characteristics of the gamma distribution, we propose a flexible method for estimating odds ratios from pooled measurements of mixed and matched status. We use simulation studies to compare consistency and efficiency of risk effect estimates from our proposed methods to existing methods. We then demonstrate the efficacy of our method applied to an analysis of pregnancy outcomes and pooled cytokine concentrations. Our proposed approach contributes to the toolkit of available methods for analyzing odds ratios of a pooled exposure, without restricting pools to be matched on a specific outcome.     

Small area estimation for semicontinuous skewed spatial data: An application to the grape wine production in Tuscany

Linear‐mixed models are frequently used to obtain model‐based estimators in small area estimation (SAE) problems. Such models, however, are not suitable when the target variable exhibits a point mass at zero, a highly skewed distribution of the nonzero values and a strong spatial structure. In this paper, a SAE approach for dealing with such variables is suggested. We propose a two‐part random effects SAE model that includes a correlation structure on the area random effects that appears in the two parts and incorporates a bivariate smooth function of the geographical coordinates of units. To account for the skewness of the distribution of the positive values of the response variable, a Gamma model is adopted. To fit the model, to get small area estimates and to evaluate their precision, a hierarchical Bayesian approach is used. The study is motivated by a real SAE problem. We focus on estimation of the per‐farm average grape wine production in Tuscany, at subregional level, using the Farm Structure Survey data. Results from this real data application and those obtained by a model‐based simulation experiment show a satisfactory performance of the suggested SAE approach.     

Alteration of phase–phase coupling between theta and gamma rhythms in a depression-model of rats

Alterations in oscillatory brain activity are strongly correlated with cognitive performance in various physiological rhythms, especially the theta and gamma rhythms. In this study, we investigated the coupling relationship of neural activities between thalamus and medial prefrontal cortex (mPFC) by measuring the phase interactions between theta and gamma oscillations in a depression model of rats. The phase synchronization analysis showed that the phase locking at theta rhythm was weakened in depression. Furthermore, theta-gamma phase locking at n:m (1:6) ratio was found between thalamus and mPFC, while it was diminished in depression state. In addition, the analysis of coupling direction based on phase dynamics showed that the unidirectional influence from thalamus to mPFC was diminished in depression state only in theta rhythm, while it was partly recovered after the memantine treatment in a depression model of rats. The results suggest that the effects of depression on cognitive deficits are modulated via profound alterations in phase information transformation of theta rhythm and theta-gamma phase coupling.     

Changes of cerebral gamma glutamyltransferase activities after treatment with exogenous inducers

The activity of gamma-glutamyltransferase localized in isolated brain synaptic membranes- and microvessels-enriched fractions was assayed after treatment of rats with either phenobarbital or ethanol. Phenobarbital increased the activity of gamma-glutamyltransferase in microvessels, without alteration of synaptic membranes activity. An increase of enzyme activity was also obtained after a chronic intoxication with ethanol. These results suggest that the isoform of gamma-glutamyltransferase localized in brain microvessels may respond to exogenous inducers.     

Definitions of state variables and state space for brain-computer interface

Neocortical state variables are defined and evaluated at three levels: microscopic using multiple spike activity (MSA), mesoscopic using local field potentials (LFP) and electrocorticograms (ECoG), and macroscopic using electroencephalograms (EEG) and brain imaging. Transactions between levels occur in all areas of cortex, upwardly by integration (abstraction, generalization) and downwardly by differentiation (speciation). The levels are joined by circular causality: microscopic activity upwardly creates mesoscopic order parameters, which downwardly constrain the microscopic activity that creates them. Integration dominates in sensory cortices. Microscopic activity evoked by receptor input in sensation induces emergence of mesoscopic activity in perception, followed by integration of perceptual activity into macroscopic activity in concept formation. The reverse process dominates in motor cortices, where the macroscopic activity embodying the concepts supports predictions of future states as goals. These macroscopic states are conceived to order mesoscopic activity in patterns that constitute plans for actions to achieve the goals. These planning patterns are conceived to provide frames in which the microscopic activity evolves in trajectories that adapted to the immediate environmental conditions detected by new stimuli. This circular sequence forms the action-perception cycle. Its upward limb is understood through correlation of sensory cortical activity with behavior. Now brain-machine interfaces (BMI) offer a means to understand the downward sequence through correlation of behavior with motor cortical activity, beginning with macroscopic goal states and concluding with recording of microscopic MSA trajectories that operate neuroprostheses. Part 1 develops a hypothesis that describes qualitatively the neurodynamics that supports the action-perception cycle and derivative reflex arc. Part 2 describes episodic, “cinematographic” spatial pattern formation and predicts some properties of the macroscopic and mesoscopic frames by which the embedded trajectories of the microscopic activity of cortical sensorimotor neurons might be organized and controlled. URL: http://sulcus.berkeley.edu     

Dependency analysis of frequency and strength of gamma oscillations on input difference between excitatory and inhibitory neurons

It has been found that gamma oscillations and the oscillation frequencies are regulated by the properties of external stimuli in many biology experimental researches. To unveil the underlying mechanism, firstly, we reproduced the experimental observations in an excitatory/inhibitory (E/I) neuronal network that the oscillation became stronger and moved to a higher frequency band (gamma band) with the increasing of the input difference between E/I neurons. Secondly, we found that gamma oscillation was induced by the unbalance between positive and negative synaptic currents, which was caused by the input difference between E/I neurons. When this input difference became greater, there would be a stronger gamma oscillation (i.e., a higher peak power in the power spectrum of the population activity of neurons). Further investigation revealed that the frequency dependency of gamma oscillation on the input difference between E/I neurons could be explained by the well-known mechanisms of inter-neuron-gamma (ING) and pyramidal-interneuron-gamma (PING). Finally, we derived mathematical analysis to verify the mechanism of frequency regulations and the results were consistent with the simulation results. The results of this paper provide a possible mechanism for the external stimuli-regulated gamma oscillations.     

The effect of gamma radiation on breaking of dormancy in Phycomyces spores

Dormant sporangiospores of Phycomyces blakesleeanus were activated by Cs-137 gamma rays. After a dose of about 300 krad, between 80 and 90% of the spores germinated normally. However, further development of the mycelium was inhibited. Even with dry spores a partial activation was obtained. Activation by gamma rays was not accompanied by an increase in trehalase activity.