A maximum entropy algorithm for rhythmic analysis of genome-wide expression patterns.

We introduce a maximum entropy-based analysis technique for extracting and characterizing rhythmic expression profiles from DNA microarray hybridization data. These patterns are clues to discovering genes implicated in cell-cycle, circadian, and other periodic biological processes. The algorithm, implemented in a program called ENRAGE (Entropy-based Rhythmic Analysis of Gene Expression), treats the task of estimating an expression profile's periodicity and phase as a simultaneous bicriterion optimization problem.

The effect of anthrax bioterrorism on emergency department presentation.

Study Objective: From September through December 2001, 22 Americans were diagnosed with anthrax, prompting widespread national media attention and public concern over bioterrorism. The purpose of this study was to determine the effect of the threat of anthrax bioterrorism on patient presentation to a West Coast emergency department (ED).

Methods: This survey was conducted at an urban county ED in Oakland, CA between December 15, 2001 and February 15, 2002.

PSEUDO-RESPONSE REGULATOR 7 and 9 are partially redundant genes essential for the temperature responsiveness of the Arabidopsis circadian clock.

Environmental time cues, such as photocycles (light/dark) and thermocycles (warm/cold), synchronize (entrain) endogenous biological clocks to local time. Although much is known about entrainment of the Arabidopsis thaliana clock to photocycles, the determinants of thermoperception and entrainment to thermocycles are not known. The Arabidopsis PSEUDO-RESPONSE REGULATOR (PRR) genes, including the clock component TIMING OF CAB EXPRESSION 1/PRR1, are related to bacterial, fungal, and plant response regulators but lack the conserved Asp that is normally phosphorylated by an upstream sensory kinase.

Two functional but noncomplementing Drosophila tyrosine decarboxylase genes: distinct roles for neural tyramine and octopamine in female fertility.

The trace biogenic amine tyramine is present in the nervous systems of animals ranging in complexity from nematodes to mammals. Tyramine is synthesized from tyrosine by the enzyme tyrosine decarboxylase (TDC), a member of the aromatic amino acid family, but this enzyme has not been identified in Drosophila or in higher animals. To further clarify the roles of tyramine and its metabolite octopamine, we have cloned two TDC genes from Drosophila melanogaster, dTdc1 and dTdc2.

DeltaFosB: a molecular switch for long-term adaptation in the brain.

DeltaFosB is a unique transcription factor that plays an essential role in long-term adaptive changes in the brain associated with diverse conditions, such as drug addiction, Parkinson's disease, depression, and antidepressant treatment. It is induced in brain, in a region- and cell-type-specific manner by many types of chronic perturbations. Once induced, it persists for long periods of time due to its unusual stability.

The Arabidopsis thaliana clock.

A combination of forward and reverse genetic approaches together with transcriptome-scale gene expression analyses have allowed the elaboration of a model for the Arabidopsis thaliana circadian clock. The working model largely conforms to the expected negative feedback loop model that has emerged from studies in other model systems. Although a core loop has emerged, it is clear that additional components remain to be identified and that the workings of the Arabidopsis clock have been established only in outline.

Two interdependent TRPV channel subunits, inactive and Nanchung, mediate hearing in Drosophila.

Hearing in Drosophila depends on the transduction of antennal vibration into receptor potentials by ciliated sensory neurons in Johnston's organ, the antennal chordotonal organ. We previously found that a Drosophila protein in the vanilloid receptor subfamily (TRPV) channel subunit, Nanchung (NAN), is localized to the chordotonal cilia and required to generate sound-evoked potentials (Kim et al., 2003).

A prospective, population-based study of the epidemiology and outcome of out-of-hospital pediatric cardiopulmonary arrest.

Background: This study reports the epidemiologic features, survival rates, and neurologic outcomes of the largest population-based series of pediatric out-of-hospital cardiopulmonary arrest patients with prospectively collected data.

Methods: Secondary analysis of data from a prospective, interventional trial of out-of-hospital pediatric airway management conducted from 1994 to 1997 (Gausche M, Lewis RJ, Stratton SJ, et al. JAMA.

SPINDLY and GIGANTEA interact and act in Arabidopsis thaliana pathways involved in light responses, flowering, and rhythms in cotyledon movements.

SPINDLY (SPY) is a negative regulator of gibberellin signaling in Arabidopsis thaliana that also functions in previously undefined pathways. The N terminus of SPY contains a protein-protein interaction domain consisting of 10 tetratricopeptide repeats (TPRs). GIGANTEA (GI) was recovered from a yeast two-hybrid screen for proteins that interact with the TPR domain.

Enhanced fitness conferred by naturally occurring variation in the circadian clock.

Natural variation in clock parameters is necessary for the circadian clock to contribute to organismal fitness over a broad geographic range. Considerable variation is evident in the period, phase, and amplitude of 150 Arabidopsis accessions, and the period length is correlated with the day length at the latitude of origin, implying the adaptive significance of correctly regulated circadian timing. Quantitative trait loci analysis of recombinant inbred lines indicates that multiple loci interact to determine period, phase, and amplitude.

Regulation of gene expression and cocaine reward by CREB and DeltaFosB.

DeltaFosB (a truncated form of FosB) and CREB (cAMP response element binding protein) are transcription factors induced in the brain's reward pathways after chronic exposure to drugs of abuse. However, their mechanisms of action and the genes they regulate remain unclear. Using microarray analysis in the nucleus accumbens of inducible transgenic mice, we found that CREB and a dominant-negative CREB have opposite effects on gene expression, as do prolonged expression of DeltaFosB and the activator protein-1 (AP-1) antagonist DeltacJun.

Phase-independent rhythmic analysis of genome-wide expression patterns.

We introduce a model-based analysis technique for extracting and characterizing rhythmic expression profiles from genome-wide DNA microarray hybridization data. These patterns are clues to discovering rhythmic genes implicated in cell-cycle, circadian, or other biological processes. The algorithm, implemented in a program called RAGE (Rhythmic Analysis of Gene Expression), decouples the problems of estimating a pattern's wavelength and phase.

Knee strength after total knee arthroplasty.

Fifty-two knees in normal healthy subjects and 32 knees more than 2 years after total knee arthroplasty (TKA) were evaluated. Average isometric extension peak torque values in TKA patients were reduced by up to 30.7% (P=.

Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis.

The circadian clock synchronizes the internal biology of an organism with the environment and has been shown to be widespread among organisms. Microarray experiments have shown that the circadian clock regulates mRNA abundance of about 10% of the transcriptome in plants, invertebrates, and mammals. In contrast, the circadian clock regulates the transcription of the virtually all cyanobacterial genes.

Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity.

Circadian rhythms are widespread in nature and reflect the activity of an endogenous biological clock. In metazoans, the circadian system includes a central circadian clock in the brain as well as distinct clocks in peripheral tissues such as the retina or liver. Similarly, plants have distinct clocks in different cell layers and tissues.

Phase-specific circadian clock regulatory elements in Arabidopsis.

We have defined a minimal Arabidopsis CATALASE 3 (CAT3) promoter sufficient to drive evening-specific circadian transcription of a LUCIFERASE reporter gene. Deletion analysis and site-directed mutagenesis reveal a circadian response element, the evening element (EE: AAAATATCT), that is necessary for evening-specific transcription. The EE differs only by a single base pair from the CIRCADIAN CLOCK ASSOCIATED 1-binding site (CBS: AAAAAATCT), which is important for morning-specific transcription.

The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis.

Arabidopsis displays circadian rhythms in stomatal aperture, stomatal conductance, and CO(2) assimilation, each of which peaks around the middle of the day. The rhythmic opening and closing of stomata confers a rhythm in sensitivity and resistance, respectively, to the toxic gas sulfur dioxide. Using this physiological assay as a basis for a mutant screen, we isolated mutants with defects in circadian timing.

The effect of total knee arthroplasty design on extensor mechanism function.

The effect of total knee arthroplasty design on extensor mechanism function was evaluated prospectively in a consecutive, single-surgeon series. Group 1 knees (n = 83) were implanted with a prosthesis that has a multiradius femoral component, and group 2 knees (n = 101) were implanted with a femoral prosthesis that has a single flexion-extension axis. Group 2 knees gained flexion more rapidly: At 6 weeks, the average flexion for was 94.

The Arabidopsis circadian system.

Rhythms with periods of approximately 24 hr are widespread in nature. Those that persist in constant conditions are termed circadian rhythms and reflect the activity of an endogenous biological clock. Plants, including Arabidopsis, are richly rhythmic.

CIRCADIAN RHYTHMS IN PLANTS.

Circadian rhythms, endogenous rhythms with periods of approximately 24 h, are widespread in nature. Although plants have provided many examples of rhythmic outputs and our understanding of photoreceptors of circadian input pathways is well advanced, studies with plants have lagged in the identification of components of the central circadian oscillator. Nonetheless, genetic and molecular biological studies, primarily in Arabidopsis, have begun to identify the components of plant circadian systems at an accelerating pace.

The John Charnley Award. Wear is a function of use, not time.

Polyethylene wear (linear penetration) in 37 hip replacements was assessed from digital images using a validated two-dimensional, edge detection-based computer algorithm. Patient activity was assessed with a pedometer, a step activity monitor and a simple visual analog scale. Joint use was related to wear at the 90% confidence level.

Integrated temporal regulation of the photorespiratory pathway. Circadian regulation of two Arabidopsis genes encoding serine hydroxymethyltransferase.

The photorespiratory pathway is comprised of enzymes localized within three distinct cellular compartments: chloroplasts, peroxisomes, and mitochondria. Photorespiratory enzymes are encoded by nuclear genes, translated in the cytosol, and targeted into these distinct subcellular compartments. One likely means by which to regulate the expression of the genes encoding photorespiratory enzymes is coordinated temporal control.

Relationship between body mass index and activity in hip or knee arthroplasty patients.

The weight of patients has not been demonstrated to have a consistent effect on the rate of polyethylene wear in clinical studies of total joint replacement. For this reason, we analyzed the relationship between quantitative activity, measured with a pedometer, and body mass index, a measure of obesity. Data were acquired for 209 individuals, 22-82 years of age; all were independent community walkers.

Factors contributing to rapid wear and osteolysis in hips with modular acetabular bearings made of hylamer.

There have been several reports of osteolysis associated with rapid wear of Hylamer. A detailed analysis of retrieved implants and tissues can identify factors contributing to rapid wear and osteolysis. The mean linear wear rate of 12 liners was 0.