University of New Mexico

About: University of New Mexico is a education organization based out in Albuquerque, New Mexico, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 28870 authors who have published 64767 publications receiving 2578371 citations. The organization is also known as: UNM & Universitatis Novus Mexico.

How many bootstrap replicates are necessary

Abstract: Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on one of the most popular, maximum likelihood (ML). Because ML inference is so computationally demanding, it has proved too expensive to date to assess the impact of the number of replicates used in BS on the relative accuracy of the support values. For the same reason, a rather small number (typically 100) of BS replicates are computed in real-world studies. Stamatakis et al. recently introduced a BS algorithm that is 1 to 2 orders of magnitude faster than previous techniques, while yielding qualitatively comparable support values, making an experimental study possible. In this article, we propose stopping criteria--that is, thresholds computed at runtime to determine when enough replicates have been generated--and we report on the first large-scale experimental study to assess the effect of the number of replicates on the quality of support values, including the performance of our proposed criteria. We run our tests on 17 diverse real-world DNA--single-gene as well as multi-gene--datasets, which include 125-2,554 taxa. We find that our stopping criteria typically stop computations after 100-500 replicates (although the most conservative criterion may continue for several thousand replicates) while producing support values that correlate at better than 99.5% with the reference values on the best ML trees. Significantly, we also find that the stopping criteria can recommend very different numbers of replicates for different datasets of comparable sizes. Our results are thus twofold: (i) they give the first experimental assessment of the effect of the number of BS replicates on the quality of support values returned through BS, and (ii) they validate our proposals for stopping criteria. Practitioners will no longer have to enter a guess nor worry about the quality of support values; moreover, with most counts of replicates in the 100-500 range, robust BS under ML inference becomes computationally practical for most datasets. The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2, and BS with our stopping criteria is included in the latest release of RAxML v7.2.5, available at http://wwwkramer.in.tum.de/exelixis/software.html.

Ecohydrological implications of woody plant encroachment

Abstract: Increases in the abundance or density of woody plants in historically semiarid and arid grassland ecosystems have important ecological, hydrological, and socioeconomic implications. Using a simplified water-balance model, we propose a framework for con- ceptualizing how woody plant encroachment is likely to affect components of the water cycle within these ecosystems. We focus in particular on streamflow and the partitioning of evapotranspiration into evaporation and transpiration. On the basis of this framework, we suggest that streamflow and evaporation processes are affected by woody plant en- croachment in different ways, depending on the degree and seasonality of aridity and the availability of subsurface water. Differences in landscape physiography, climate, and runoff mechanisms mediate the influence of woody plants on hydrological processes. Streamflow is expected to decline as a result of woody plant encroachment in landscapes dominated by subsurface flow regimes. Similarly, encroachment of woody plants can be expected to produce an increase in the fractional contribution of bare soil evaporation to evapotrans- piration in semiarid ecosystems, whereas such shifts may be small or negligible in both subhumid and arid ecosystems. This framework for considering the effects of woody plant encroachment highlights important ecological and hydrological interactions that serve as a basis for predicting other ecological aspects of vegetation change—such as potential changes in carbon cycling within an ecosystem. In locations where woody plant encroach- ment results in increased plant transpiration and concurrently the availability of soil water is reduced, increased accumulation of carbon in soils emerges as one prediction. Thus, explicitly considering the ecohydrological linkages associated with vegetation change pro- vides needed information on the consequences of woody plant encroachment on water yield, carbon cycling, and other processes.

Terahertz compressive imaging with metamaterial spatial light modulators

Abstract: Active metamaterials have been used to realize terahertz imaging with a single-pixel detector Compressive techniques permit high-fidelity images to be acquired at high frame rates The technique involves no moving parts and yields improved signal-to-noise ratios over standard raster scanning techniques