Statistical Phylogenetic Tree Analysis Using Differences of Means

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling. Our method uses difference of means to compare two distributions of trees, after embedding trees in a vector space. Bootstrapping alignment columns can then be applied to obtain p-values. To compute distances between means, we employ a "kernel trick" which speeds up distance calculations when trees are embedded in a high-dimensional feature space, e.g. splits or quartets feature space. In this pilot study, first we test our statistical method's ability to distinguish between sets of gene trees generated under coalescence models with species trees of varying dissimilarity. We follow our simulation results with applications to various data sets of gophers and lice, grasses and their endophytes, and different fungal genes from the same genome. A companion toolkit, {\tt Phylotree}, is provided to facilitate computational experiments.Comment: 17 pages, 6 figure

Statistical Computations with AstroGrid and the Grid

We outline our first steps towards marrying two new and emerging technologies; the Virtual Observatory (e.g, AstroGrid) and the computational grid. We discuss the construction of VOTechBroker, which is a modular software tool designed to abstract the tasks of submission and management of a large number of computational jobs to a distributed computer system. The broker will also interact with the AstroGrid workflow and MySpace environments. We present our planned usage of the VOTechBroker in computing a huge number of n-point correlation functions from the SDSS, as well as fitting over a million CMBfast models to the WMAP data.Comment: Invited talk to appear in "Proceedings of PHYSTAT05: Statistical Problems in Particle Physics, Astrophysics and Cosmology

Quantifying Inter- and Intra-Population Niche Variability Using Hierarchical Bayesian Stable Isotope Mixing Models

Variability in resource use defines the width of a trophic niche occupied by a population. Intra-population variability in resource use may occur across hierarchical levels of population structure from individuals to subpopulations. Understanding how levels of population organization contribute to population niche width is critical to ecology and evolution. Here we describe a hierarchical stable isotope mixing model that can simultaneously estimate both the prey composition of a consumer diet and the diet variability among individuals and across levels of population organization. By explicitly estimating variance components for multiple scales, the model can deconstruct the niche width of a consumer population into relevant levels of population structure. We apply this new approach to stable isotope data from a population of gray wolves from coastal British Columbia, and show support for extensive intra-population niche variability among individuals, social groups, and geographically isolated subpopulations. The analytic method we describe improves mixing models by accounting for diet variability, and improves isotope niche width analysis by quantitatively assessing the contribution of levels of organization to the niche width of a population

Bell's Theorem from Moore's Theorem

It is shown that the restrictions of what can be inferred from classically-recorded observational outcomes that are imposed by the no-cloning theorem, the Kochen-Specker theorem and Bell's theorem also follow from restrictions on inferences from observations formulated within classical automata theory. Similarities between the assumptions underlying classical automata theory and those underlying universally-unitary quantum theory are discussed.Comment: 12 pages; to appear in Int. J. General System

Tracking the weight of Hurricane Harvey’s stormwater using GPS data

On 26 August 2017, Hurricane Harvey struck the Gulf Coast as a category four cyclone depositing ~95 km3 of water, making it the wettest cyclone in U.S. history. Water left in Harvey’s wake should cause elastic loading and subsidence of Earth’s crust, and uplift as it drains into the ocean and evaporates. To track daily changes of transient water storage, we use Global Positioning System (GPS) measurements, finding a clear migration of subsidence (up to 21 mm) and horizontal motion (up to 4 mm) across the Gulf Coast, followed by gradual uplift over a 5-week period. Inversion of these data shows that a third of Harvey’s total stormwater was captured on land (25.7 ± 3.0 km3 ), indicating that the rest drained rapidly into the ocean at a rate of 8.2 km3 /day, with the remaining stored water gradually lost over the following 5 weeks at ~1 km3 /day, primarily by evapotranspiration. These results indicate that GPS networks can remotely track the spatial extent and daily evolution of terrestrial water storage following transient, extreme precipitation events, with implications for improving operational flood forecasts and understanding the response of drainage systems to large influxes of water

Effect of a liquid multi-vitamin-mineral supplement on anaerobic exercise performance

This is the publisher's version, also found at http://ehis.ebscohost.com/ehost/detail?sid=10f44d64-ddff-470e-a85a-b4c63b016efa%40sessionmgr10&vid=1&hid=2&bdata=JnNpdGU9ZWhvc3QtbGl2ZQ%3d%3d#db=s3h&AN=20338872The purpose of this study was to determine if supplementation with a liquid multi-vitamin/mineral would improve anaerobic exercise performance. Fourteen resistance-trained men performed a 30-second cycle sprint and one set of squat exercise on 2 separate days before and following 8 weeks of supplementation with either a liquid multi-vitamin/ mineral or a placebo. Heart rate, perceived exertion, blood lactate, peak and mean power, and rate of fatigue were determined for all tests. No differences were noted for any variable (P > 0.05). When controlling for presupplementation values, however, a decreased rate of fatigue was noted for both exercise tests following the multi-vitamin/mineral supplementation. These data suggest that in resistance trained men consuming a nutritionally sound diet, supplementation with a liquid multi-vitamin/mineral does not favorably impact most anaerobic exercise performances. Such supplementation, however, may result in a minor decreased rate of fatigue. It appears that, in terms of improved short duration anaerobic exercise performance, supplemental micronutrients may not be efficient ergogenic agents for well-trained individuals consuming an adequate diet

Estimating the economic impacts of climate change on 16 major US fisheries

Observational evidence shows marine species are shifting their geographic distribution in response to warming ocean temperatures. These shifts have implications for the US fisheries and seafood consumers. The analysis presented here employs a two-stage inverse demand model to estimate the consumer welfare impacts of projected increases or decreases in commercial landings for 16 US fisheries from 2021 to 2100, based on the predicted changes in thermally available habitat. The fisheries analyzed together account for 56% of the current US commercial fishing revenues. The analysis compares welfare impacts under two climate scenarios: a high emissions case that assumes limited efforts to reduce atmospheric greenhouse gas and a low emissions case that assumes more stringent mitigation. The present value of consumer surplus impacts when discounted at 3% is a net loss of $2.1 billion (2018 US$) in the low emissions case and $4.2 billion in the high emissions scenario. Projected annual losses reach$278–901 million by 2100

Association Between Chronic Hepatitis C Virus Infection and Myocardial Infarction Among People Living With HIV in the United States.

Hepatitis C virus (HCV) infection is common among people living with human immunodeficiency virus (PLWH). Extrahepatic manifestations of HCV, including myocardial infarction (MI), are a topic of active research. MI is classified into types, predominantly atheroembolic type 1 MI (T1MI) and supply-demand mismatch type 2 MI (T2MI). We examined the association between HCV and MI among patients in the Centers for AIDS Research (CFAR) Network of Integrated Clinical Systems, a US multicenter clinical cohort of PLWH. MIs were centrally adjudicated and categorized by type using the Third Universal Definition of Myocardial Infarction. We estimated the association between chronic HCV (RNA+) and time to MI while adjusting for demographic characteristics, cardiovascular risk factors, clinical characteristics, and history of injecting drug use. Among 23,407 PLWH aged ≥18 years, there were 336 T1MIs and 330 T2MIs during a median of 4.7 years of follow-up between 1998 and 2016. HCV was associated with a 46% greater risk of T2MI (adjusted hazard ratio (aHR) = 1.46, 95% confidence interval (CI): 1.09, 1.97) but not T1MI (aHR = 0.87, 95% CI: 0.58, 1.29). In an exploratory cause-specific analysis of T2MI, HCV was associated with a 2-fold greater risk of T2MI attributed to sepsis (aHR = 2.01, 95% CI: 1.25, 3.24). Extrahepatic manifestations of HCV in this high-risk population are an important area for continued research

An internet-based intervention with brief nurse support to manage obesity in primary care (POWeR+): a pragmatic, parallel-group, randomised controlled trial

Background The obesity epidemic has major public health consequences. Expert dietetic and behavioural counselling with intensive follow-up is effective, but resource requirements severely restrict widespread implementation in primary care, where most patients are managed. We aimed to estimate the effectiveness and cost-effectiveness of an internet-based behavioural intervention (POWeR+) combined with brief practice nurse support in primary care. Methods We did this pragmatic, parallel-group, randomised controlled trial at 56 primary care practices in central and south England. Eligible adults aged 18 years or older with a BMI of 30 kg/m2 or more (or ≥28 kg/m2 with hypertension, hypercholesterolaemia, or diabetes) registered online with POWeR+—a 24 session, web-based, weight management intervention lasting 6 months. After registration, the website automatically randomly assigned patients (1:1:1), via computer-generated random numbers, to receive evidence-based dietetic advice to swap foods for similar, but healthier, choices and increase fruit and vegetable intake, in addition to 6 monthly nurse follow-up (control group); web-based intervention and face-to-face nurse support (POWeR+Face-to-face [POWeR+F]; up to seven nurse contacts over 6 months); or web-based intervention and remote nurse support (POWeR+Remote [POWeR+R]; up to five emails or brief phone calls over 6 months). Participants and investigators were masked to group allocation at the point of randomisation; masking of participants was not possible after randomisation. The primary outcome was weight loss averaged over 12 months. We did a secondary analysis of weight to measure maintenance of 5% weight loss at months 6 and 12. We modelled the cost-effectiveness of each intervention. We did analysis by intention to treat, with multiple imputation for missing data. This trial is registered as an International Standard Randomised Controlled Trial, number ISRCTN21244703. Findings Between Jan 30, 2013, and March 20, 2014, 818 participants were randomly assigned to the control group (n=279), the POWeR+F group (n=269), or the POWeR+R group (n=270). Weight loss averaged over 12 months was recorded in 666 (81%) participants. The control group lost almost 3 kg over 12 months (crude mean weight: baseline 104·38 kg [SD 21·11; n=279], 6 months 101·91 kg [19·35; n=136], 12 months 101·74 kg [19·57; n=227]). The primary imputed analysis showed that compared with the control group, patients in the POWeR+F group achieved an additional weight reduction of 1·5 kg (95% CI 0·6–2·4; p=0·001) averaged over 12 months, and patients in the POWeR+R group achieved an additional 1·3 kg (0·34–2·2; p=0·007). 21% of patients in the control group had maintained a clinically important 5% weight reduction at month 12, compared with 29% of patients in the POWeR+F group (risk ratio 1·56, 0·96–2·51; p=0·070) and 32% of patients in the POWeR+R group (1·82, 1·31–2·74; p=0·004). The incremental overall cost to the health service per kg weight lost with the POWeR+ interventions versus the control strategy was £18 (95% CI −129 to 195) for POWeR+F and –£25 (−268 to 157) for POWeR+R; the probability of being cost-effective at a threshold of £100 per kg lost was 88% and 98%, respectively. No adverse events were reported. Interpretation Weight loss can be maintained in some individuals by use of novel written material with occasional brief nurse follow-up. However, more people can maintain clinically important weight reductions with a web-based behavioural program and brief remote follow-up, with no increase in health service costs. Future research should assess the extent to which clinically important weight loss can be maintained beyond 1 year