Fast, Exact Bootstrap Principal Component Analysis for p>1 million

Many have suggested a bootstrap procedure for estimating the sampling variability of principal component analysis (PCA) results. However, when the number of measurements per subject ($p$) is much larger than the number of subjects ($n$), the challenge of calculating and storing the leading principal components from each bootstrap sample can be computationally infeasible. To address this, we outline methods for fast, exact calculation of bootstrap principal components, eigenvalues, and scores. Our methods leverage the fact that all bootstrap samples occupy the same $n$-dimensional subspace as the original sample. As a result, all bootstrap principal components are limited to the same $n$-dimensional subspace and can be efficiently represented by their low dimensional coordinates in that subspace. Several uncertainty metrics can be computed solely based on the bootstrap distribution of these low dimensional coordinates, without calculating or storing the $p$-dimensional bootstrap components. Fast bootstrap PCA is applied to a dataset of sleep electroencephalogram (EEG) recordings ($p=900$, $n=392$), and to a dataset of brain magnetic resonance images (MRIs) ($p\approx$ 3 million, $n=352$). For the brain MRI dataset, our method allows for standard errors for the first 3 principal components based on 1000 bootstrap samples to be calculated on a standard laptop in 47 minutes, as opposed to approximately 4 days with standard methods.Comment: 25 pages, including 9 figures and link to R package. 2014-05-14 update: final formatting edits for journal submission, condensed figure

Hard x ray highlights of AR 5395

Active Region 5395 produced an exceptional series of hard x ray bursts notable for their frequency, intensity, and impulsivity. Over the two weeks from March 6 to 19, 447 hard x ray flares were observed by the Hard X Ray Burst Spectrometer on Solar Maximum Mission (HXRBS/SMM), a rate of approx. 35 per day which exceeded the previous high by more than 50 percent. During one 5 day stretch, more than 250 flares were detected, also a new high. The three largest GOES X-flares were observed by HXRBS and had hard x ray rates over 100,000 s(exp -1) compared with only ten flares above 100,000(exp -1) during the previous nine years of the mission. An ongoing effort for the HXRBS group has been the correlated analysis of hard x ray data with flare data at other wavelengths with the most recent emphasis on those measurements with spatial information. During a series of bursts from AR 5395 at 1644 to 1648 UT on 12 March 1989, simultaneous observations were made by HXRBS and UVSP (Ultra Violet Spectrometer Polarimeter) on SMM, the two-element Owens Valley Radio Observatory (OVRO) interferometric array, and R. Canfield's H-alpha Echelle spectrograph at the National Solar Observatory at Sacramento Peak. The data show strong correlations in the hard x ray, microwave, and UV lightcurves. This event will be the subject of a combined analysis

WTO and GMOs: Analyzing the European Community\u27s Recent Regulations Covering the Labeling of Genetically Modified Organisms

This Note explores the compatibility of the EC\u27s GMO regulations within the framework of the Agreement on the Application of Sanitary and Phytosanitary Measures ( SPS Agreement ), the Agreement on Technical Barriers to Trade ( TBT Agreement ), and the General Agreement on Tariffs and Trade 1994 ( GATT 1994 or GAT ), all integral parts of the WTO Agreement. Part II presents arguments for or against the use of GM-products. Part III explores the concept of ecolabeling by analyzing the general goals of such programs, including the economic theory behind green consumerism and the characteristics necessary for effective schemes. Part IV describes the core objectives and features of the EC regulations. To provide a framework for analyzing the EC regulations under the WTO regime, Part V sorts eco-labeling schemes into different categories. Part VI examines the legality of the EC\u27s regulations under the SPS Agreement, the TBT Agreement and GATT 1994. Finally, Part VII presents a proposal for a trade-sensitive regime. This Note illustrates that the EC regulations run afoul of several WTO provisions, but argues that it is possible to develop an eco-labeling program to assuage consumer concerns over GMOs without violating WTO Agreement and without the need to resort to a new watered-down treaty

WTO and GMOs: Analyzing the European Community\u27s Recent Regulations Covering the Labeling of Genetically Modified Organisms

This Note explores the compatibility of the EC\u27s GMO regulations within the framework of the Agreement on the Application of Sanitary and Phytosanitary Measures ( SPS Agreement ), the Agreement on Technical Barriers to Trade ( TBT Agreement ), and the General Agreement on Tariffs and Trade 1994 ( GATT 1994 or GAT ), all integral parts of the WTO Agreement. Part II presents arguments for or against the use of GM-products. Part III explores the concept of ecolabeling by analyzing the general goals of such programs, including the economic theory behind green consumerism and the characteristics necessary for effective schemes. Part IV describes the core objectives and features of the EC regulations. To provide a framework for analyzing the EC regulations under the WTO regime, Part V sorts eco-labeling schemes into different categories. Part VI examines the legality of the EC\u27s regulations under the SPS Agreement, the TBT Agreement and GATT 1994. Finally, Part VII presents a proposal for a trade-sensitive regime. This Note illustrates that the EC regulations run afoul of several WTO provisions, but argues that it is possible to develop an eco-labeling program to assuage consumer concerns over GMOs without violating WTO Agreement and without the need to resort to a new watered-down treaty

Sex-specific investment in incubation and the reproductive biology of two tropical antbird species

Paternal care has been neglected in behavioral studies because it is rare among most animals. Birds express wide variation in male care across a broad life-history gradient, but such variation among species remains poorly explored. At the same time, contributions of male assistance with incubation have been largely overlooked with the assumption that incubation is a time of low parental energy expenditure. We compared male versus female biparental incubation effort between two tropical antbird species in the northern Andes of Venezuela. We found that males and females apportion reproductive effort differently between these two species, but that male contributions of time and incubation effort were generally greater than for north temperate species which exhibit different life-history strategies. Males spent an equal or greater amount of time incubating, yet maintained lower egg temperatures than females during different age-specific stages of the incubation period. Despite sex differences in incubation temperatures, males rewarmed cold clutches at similar rates to females suggesting similar sex-specific physiological incubation abilities. For the first time in a nidicolous species, we found that temperatures experienced by developing embryos increased with age of eggs independent of male and female time spent on the nest. Our results suggest that males may benefit embryo development by minimizing time eggs experience cold temperatures during female absences, and concurrently benefit female physiological condition for future nesting efforts. Lastly, we report standardized measures of reproductive traits in these two endemic tropical species in hope of improving data collection efforts outside of North America. Standardized measures of reproductive traits are essential for improving our understanding of reproductive biology and avian life-history evolution among different regions of the world. The Tropical Andes are among one of the most species-rich areas in the world and represent an area of critical conservation concern. Yet, for many endemic taxa inhabiting this region even basic descriptions of reproductive traits are entirely absent. This study extends the range of variation in reproductive strategies among a broader range of species among geographical regions

Potential Cardio-protective Effects of Psoriasis Medications

Psoriasis management can be challenging, complicated sometimes by being associated with other systematic inflammatory diseases including metabolic syndrome, myocardial infarction, hypertension, obesity, diabetes mellitus, and hyperlipidemia. Of particularly concern is its cardiovascular linkage. It is noteworthy and reassuring that some therapeutic options for psoriasis may be cardio-protective. We highlight phototherapy, methotrexate, and TNF alpha inhibitors and other biological agents for psoriasis that may lower the risk of cardiovascular events. Ways to reduce cardiovascular risk in patients with psoriasis should be encouraged. We concur with the conclusion that long-term study is necessary to assess the risks and benefits of biologic therapy, but that persons with preexistent cardiovascular disease or at high risk for it might benefit from medication with cardio-preventive value.</p