Peak Ventilation Reference Standards from Exercise Testing: From the FRIEND Registry

Peak Ventilation Reference Standards from Exercise Testing: From the FRIEND Registry. Med. Sci. Sports Exerc., Vol. 50, No. 12, pp. 2603–2608, 2018. Purpose: Cardiopulmonary exercise testing (CPX) provides valuable clinical information, including peak ventilation (V˙ Epeak), which has been shown to have diagnostic and prognostic value in the assessment of patients with underlying pulmonary disease. This report provides reference standards for V˙ Epeak derived from CPX on treadmills in apparently healthy individuals. Methods: Nine laboratories in the United States experienced in CPX administration with established quality control procedures contributed to the Fitness Registry and the Importance of Exercise National Database from 2014 to 2017. Data from 5232 maximal exercise tests from men and women without cardiovascular or pulmonary disease were used to create percentiles ofV˙ Epeak for both men and women by decade between 20 and 79 yr. Additionally, prediction equations were developed for V˙ Epeak using descriptive information. Results: V˙ Epeak was found to be significantly different between men and women and across age groups (P G 0.05). The rate of decline in V˙ Epeak was 8.0% per decade for both men and women. A stepwise regression model of 70% of the sample revealed that sex, age, and height were significant predictors ofV˙ Epeak. The equation was cross-validated with data from the remaining 30% of the sample with a final equation developed from the full sample (r = 0.73). Additionally, a linear regression model revealed forced expiratory volume in 1 s significantly predicted V˙ Epeak (r = 0.73). Conclusions: Reference standards were developed for V˙ Epeak for the United States population. Cardiopulmonary exercise testing laboratories will be able to provide interpretation of V˙ Epeak from these age and sex-specific percentile reference values or alternatively can use these nonexercise prediction equations incorporating sex, age, and height or with a single predictor of forced expiratory volume in 1 s

LASR-Guided Stellar Photometric Variability Subtraction: The Linear Algorithm For Significance Reduction

We develop a technique for removing stellar variability in the light curves of $\delta$-Scuti and similar stars. Our technique, which we name the Linear Algorithm for Significance Reduction (LASR), subtracts oscillations from a time series by minimizing their statistical significance in frequency space. We demonstrate that LASR can subtract variable signals of near-arbitrary complexity and can robustly handle close frequency pairs and overtone frequencies. We demonstrate that our algorithm performs an equivalent fit as prewhitening to the straightforward variable signal of KIC 9700322. We also show that LASR provides a better fit to seismic activity than prewhitening in the case of the complex $\delta$-Scuti KOI-976.Comment: 9 pages, 5 figures, accepted for publication in Astronomy & Astrophysics. Pseudocode and github link to code included in manuscrip

Spin transfer switching of spin valve nanopillars using nanosecond pulsed currents

Spin valve nanopillars are reversed via the mechanism of spin momentum transfer using current pulses applied perpendicular to the film plane of the device. The applied pulses were varied in amplitude from 1.8 mA to 7.8 mA, and varied in duration within the range of 100 ps to 200 ns. The probability of device reversal is measured as a function of the pulse duration for each pulse amplitude. The reciprocal pulse duration required for 95% reversal probability is linearly related to the pulse current amplitude for currents exceeding 1.9 mA. For this device, 1.9 mA marks the crossover between dynamic reversal at larger currents and reversal by thermal activation for smaller currents

Experimental simulation of closed timelike curves

Closed timelike curves are among the most controversial features of modern physics. As legitimate solutions to Einstein's field equations, they allow for time travel, which instinctively seems paradoxical. However, in the quantum regime these paradoxes can be resolved, leaving closed timelike curves consistent with relativity. The study of these systems therefore provides valuable insight into nonlinearities and the emergence of causal structures in quantum mechanics-essential for any formulation of a quantum theory of gravity. Here we experimentally simulate the nonlinear behaviour of a qubit interacting unitarily with an older version of itself, addressing some of the fascinating effects that arise in systems traversing a closed timelike curve. These include perfect discrimination of non-orthogonal states and, most intriguingly, the ability to distinguish nominally equivalent ways of preparing pure quantum states. Finally, we examine the dependence of these effects on the initial qubit state, the form of the unitary interaction and the influence of decoherence

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool

BACKGROUND: The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the gene ontology have been developed. However, no existing system provides an interactively expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools are web-based or require an Internet connection, will not load local annotations files, and provide either analysis or visualization functionality, but not both. RESULTS: To address the above limitations, we have developed GOLEM (Gene Ontology Local Exploration Map), a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet at

Finding function: evaluation methods for functional genomic data

BACKGROUND: Accurate evaluation of the quality of genomic or proteomic data and computational methods is vital to our ability to use them for formulating novel biological hypotheses and directing further experiments. There is currently no standard approach to evaluation in functional genomics. Our analysis of existing approaches shows that they are inconsistent and contain substantial functional biases that render the resulting evaluations misleading both quantitatively and qualitatively. These problems make it essentially impossible to compare computational methods or large-scale experimental datasets and also result in conclusions that generalize poorly in most biological applications. RESULTS: We reveal issues with current evaluation methods here and suggest new approaches to evaluation that facilitate accurate and representative characterization of genomic methods and data. Specifically, we describe a functional genomics gold standard based on curation by expert biologists and demonstrate its use as an effective means of evaluation of genomic approaches. Our evaluation framework and gold standard are freely available to the community through our website. CONCLUSION: Proper methods for evaluating genomic data and computational approaches will determine how much we, as a community, are able to learn from the wealth of available data. We propose one possible solution to this problem here but emphasize that this topic warrants broader community discussion

Hominids adapted to metabolize ethanol long before human-directed fermentation

Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate-ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol